Think its making sense now, and then the PLX chip is taking those 8 lanes and making it appear as x16 for the GPU in Slot 4.  I think the last SLI board I had had both slots going through the PLX chip, so they both appears as x16 (or I could be making that up, memory ain't what it used to be).  Hence the confusion.
 
So then I'm all good!  Thanks much again!

sorry I posted back late
hate to sound silly  maybe I'm wrong ?  seems these boards like mine need that auxiliary  PCI / sli power  that at the bottom edge of the mother board  ?   did you have that hooked up ?
 
I seen that just looking back at this 
 
from evga joey
 
''  For this motherboard you can use any slot configuration you would like, you just won't be able to use 1x slot for your video cards. With multiple PCI-E cards we do recommend using the 6pin supplemental power connector towards the bottom of the motherboard. Adding in a sound card will not deactivate any slots, but will cause you to run at 8x/8x/8x. While running in SLI with no sound card will yield you 16x/16x performance. Please let us know if you have any other questions. ''
 
https://forums.evga.com/Z97-Classified-m2175095.aspx
 

The EVGA Z97 Classified Up Close

Along the bottom of the Z97 classified, we first see a 6-pin PCI-E connector for providing additional power to multi-GPU setups
 
http://www.overclockers.com/evga-z97-classified-motherboard-review/
 
 
https://www.evga.com/support/faq/afmviewfaq.aspx?faqid=59481
 
 
same in the review of the Z*& classy
 
''Across the bottom of the board, there really isn’t too much here honestly. On the left is a PCIe 6-pin connector for when you run multiple cards (gives an alternate power source than the 24 pin for the slots)
 
http://www.overclockers.com/evga-z87-classified-review/
 
 
like with my board makes me wonder if the motherboard voltage regulation aint so up to snuff  powering the cards slots  when you see multi card motherboards that don't have that  extra pcie power hook up ?
 
also see the 2 reviews specs on the slot configuration  is changes on the z97 for / to the better ??????
 
good luck

ya, that's what I noticed fron them 2 reviews the 97 seemed a bit improved  over the slots configuration  of the 87  .
 
I don't know   seems like if running 2 card sli just as well of on a board that got the 2 slots tied to the cpu and x8/x8  , b ut what do I know just a opinion
 
one mistake I found out on my board is if I use any 3ed slot / m2 , ect  I loose sli   [ I used all AMD board until this intel z87  all lanes on amd are through the chipset ] 
 
so  with that its now something I look at closer on how the slots are ''wired''' 
 
''
The three PCI Express 3.0 x16 slots are controlled by the CPU, with the first slot working at x16 when only one video card is installed, the first two working at x8 when two video cards are installed, and the first working at x8 and the other two working at x4 when three video cards are installed.
This configuration is somewhat different from what we’ve seen in competing products, where the third PCI Express x16 slot is 2.0, controlled by the chipset, and works at x1, x2, or x4 speed.
All three PCI Express x16 slots support the CrossFireX technology. SLI is supported only on the first two slots. The motherboard requires the installation of an auxiliary power connector from the power supply when you install more than one video card.''
 
see ?    now like this z87   the 2 primary slots are full x8/x8   off the cpu and not shared with any other slots 
 
The two PCI Express 3.0 x16 slots are controlled by the CPU, with the first slot working at x16 when only one video card is installed, and with both working at x8 when two video cards are installed.
 
with that id you any outher slots or m2 its on the chipset not interfearing with the cpu lanes as with my board 
 
personally  I guess it shows if using multi card with add in cards / m2  in any  configuration  is where a X -board pays off  with a higher cpu lane count  over the 16 you get  like say a haswell type cpu
 
plx is nice  but I guess you have to look at how its ''wired '' as well for any supprise short comings that could pop up  in a configuration
 
 
anyway glad your z97 has sorted things out for you and all's good 
 
now enjoy