Looks like a dead card to me. Sure, it stinks to get a bad card but seriously...it's not THAT widespread of an issue. I've since had 4 different 2080Ti's that were purchased and each one has been flawless for months. I did initially have 1 bad card but the RMA was quick and painless. 
 
It sucks but trust me, you'll be taken care of and you'll be back up and running. It will take some time for the very early cards to flush out of retail channels. 

SprayingMango
Looks like a dead card to me. Sure, it stinks to get a bad card but seriously...it's not THAT widespread of an issue. I've since had 4 different 2080Ti's that were purchased and each one has been flawless for months. I did initially have 1 bad card but the RMA was quick and painless. 
 
It sucks but trust me, you'll be taken care of and you'll be back up and running. It will take some time for the very early cards to flush out of retail channels. 

 
Oh I know it stinks to have to do it all over again but not sure which direction I want to head now.  Attempt one more time or slap my 780s in SLI and just frag on.  It's just a pain to change things cause I had to build a overkill loop. lol  Now I pay for it when I need to swap hardware.

AHowes
Seems strange.. all those beeps.

Did ya test this card before putting the water block on? Wires going to the card are fully seated and no wires pushed out the backside of the connector? Same with the psu side of the pci-e wire connections if it's a modular psu?

Is this a new pc case? If so its possible theirs a mb standoff in the wrong position touching something under the mb.

Card fully inserted into the pci-e slot? Not a hair crooked?

The first set of beeps are normal since I cleared the CMOS on the X99 Classified.  The secondary beeps are the odd balls which I assume says there's no GPU.
 
Unfortunately, I was too optimistic to test out the GPU in my air cool rig and wanted to get started on the long task at hand.  I should have tested it as it wouldn't have taken much of my time.  Lesson learned surely.
 
The PC it's in has been with the X99 for about half a decade now so nothing was changed other than 2 780 Hydro's to a single 2080 Ti for the time being. 
 
I seated and screwed the card in before I tubed it up.  Took a look again and it looks seated with the PCIe latch swung up which tells me it's hooked in.  With that said, you got me paranoid and I'm going to investigate this even further.  
 
Here are some angle shots I took as best as I can.
 

 

 

 
Looking at it a 3rd time, I feel it's in there because I made sure it was locked in before I proceeded with tubing it up but regardless, let me know what you guys think.

I also did change up the PSU cables and PSU ports.  It's a full modular Corsair AX1200i.

Sajin
D6 = No gpu detected.
 
Sounds like you got yourself a dead gpu. Other possibilities could be a faulty slot, or card not seated correctly.

Thanks Sajin. 
 
My last option I feel is to drain it all again, install the air cooler and test it in my air rig which I should have done the first time before I installed the block and go from there.  Than I think I'll know the culprit.

So you have changed the psu cables.. can you try other pci-e cables? Cables good? Tested with a multimeter to see if there wires correctly? 12v and ground wired correctly? Be strange but I'd want to grab the old cables first before removing the loop and block if possible.

GTXJackBauer

AHowes
So you have changed the psu cables.. can you try other pci-e cables? Cables good? Tested with a multimeter to see if there wires correctly? 12v and ground wired correctly? Be strange but I'd want to grab the old cables first before removing the loop and block if possible.

Yep, been there done that.  It's the thought that matters.  Read my posts at least dammit. 

Wow think I've read it and have posted already ideas as an attempt to assist in preventing you from going threw a whole bunch of work.

Good luck I guess.

I will break down day 2 so bare with me.
 
So I didn't want to just throw in the RMA towel in just yet so I went ahead, slapped the air cooler on the GPU and threw her in my x58 air cooled rig.  Low and behold, she came alive!
 

 
Made sure it wasn't just a tease and got more info.
 

 
 
Feeling a huge relief, I decided not to jump the gun just yet but to put in the air cooled RTX into my current main rig with the loop that I was having issues with.  The way I planned this out was to have the GPU in PCIe #1 with a CPU block right above it plugged.  I was going to use one of the amazing features on the X99 Classified where I can down clock my CPU for just enough power to boot and get into windows for example but I was only going to power up the PC for a few seconds to see if the RTX would power up, LEDs lit and fans spinning, etc.  I went ahead and saw it power up but eventually shutting down.  I figured maybe something was overheating but there was just no way.  The block on the CPU was basically passive cooling itself with some liquid plugged into it and the GPU had air cooling.  I touched around and you can barely feel any warmth whatsoever. 
 
I scratched my head in disbelief that maybe something IS wrong with the MB or the PSU.  I check around and notice my I/O X99 Shield Cover.  I remember years ago through the X99 forums of folks having issues with that thing installed causing shorts, etc.  So I decided to remove it and oddly enough, my next attempt to power up didn't have power cycles but eventually a screaming beep came on from my Aquaero telling me that there was no "flow" as there wasn't. lol  It's an alarm I've setup for the system to shut down if say I was away but anyhoo, I did test it out a few times to be sure I wasn't hallucinating.  All was looking well so I than proceeded to install the block. 
 
For the 2nd time, I removed the air cooler and reinstalled the block, cleaning both of their TIMs and reapplying.  Agonizing process to keep doing something over and over but it's part of the PC problem solving world I guess.  When you allow your frustrations and emotions take over, you lose the focus of problem solving and I know it's easier said than done but it has to be done that way.



 

 

 
I than proceeded and installed the GPU back to the loop again but this time with a bit more optimism.  I primed the pumps and bled the loop as much as I could before attempting another test to see if the GPU will power up with it installed in the loop.  This would be the first time since my last failed attempts the previous day.

Unfortunately I forgot to take a few shots of that process but amazingly, she was lit.  (Insert bad joke comment.)
 
Anyways I was so stoked and after a few hours of leaking testing, I moved her to her final destination.  I proceeded to plug in a horde's nest of USB's in the rear.  Plugged in my 3 screens via DP.  Powered her up only to get power cycles again.  Son of a gun, I've had enough of it I said to myself a few times.  It just doesn't want to play nice and throw me into a emotional roller coaster ride.  I thought to myself, what would I tell someone on the forums to do during something like this so I than began to plug only the mouse and keyboard.  PC loaded up.....I shutdown and added all of them.  PC had a hissy fit (It was probably me being echo'd off the walls and of the tower.)  Ok so now I"m thinking maybe the RTX is a gold digging high demanding princess and doesn't like all of those USB's plugged in the rear.  Nonetheless, I began unplugging each one one by one till the power cycles stopped but after every restart, the power cycling was still there.  So I figured, if I'm in windows I'm good but if I need to do a update with a restart, I'm screwed. 
 
Ok, not to bore you guys anymore, all it was was the darn turbo switch I forgot to put back into its original position when I was testing the GPU previously on air!  My PC was running down clocked and I think with much less resources as this feature is designed for extreme OC's who have very high clocks and will enable this switch to just boot up till they start benchmarking those ridiculous high clocks or LN2 or what have you. 
 
Anyways, I hit the switch, plugged everything back in and here I am.
 
Here's a final shot of her.
 

 
 
Here's a nice shot of PX1 while I had just finished running Scan.  I have no idea what I'm doing yet as I'm fairly new at this but can someone explain to me if the score I got means that's how much "+" clock I can add for an OC or that's just a score? 
 
Also, I saw 2025ish area before the test completed.  I wasn't sure if I was waiting for a OC bench lock up since I felt that look pretty high or it was testing up to the point of instability and laying off.  I sure felt like the latter and did like seeing the numbers I got. 
 
Around 1800+ I started to hear some coil whine but wasn't that bad for me and that was with the headphones off. 
 
Did some minor gaming runs, I saw 1860 constantly but again, I haven't touched any of the GPU settings other than setting the Power Target to 112% which is the max for RTX 2080 Ti Black.
 

 
 
Hope you all had a good laugh as it was a mix of misery, optimism and excitement the last 36 hours over here.  The crazy world of custom cooling and pain staking hardware swapping.    Hope you all enjoyed and learned something from this as I did.
 
Cheers!

Wow what a journey! Glad you figured it out. :) So the final issue was the cover plate on the MB?

Ok, not to bore you guys anymore, all it was was the darn turbo switch I forgot to put back into its original position when I was testing the GPU previously on air! My PC was running down clocked and I think with much less resources as this feature is designed for extreme OC's who have very high clocks and will enable this switch to just boot up till they start benchmarking those ridiculous high clocks or LN2 or what have you.

Figured it was something stupid. :/ glad shes finally running.

What's your GPU idle temps and the load temps durring like firestrike or timespy bench?

Room temp and what kind of rad for the gpu?