Running a graphics card in the lower x16 slot.

Most boards don't even function that way. I doubt it would work in most boards. Why would you want to put it in the second slot only?

I'm not really sure I would want to run it that way but it might improve cooling of a single graphics card because it's right where a front intake fan blows in most midtowers with a top mounted PSU. I was just curious if it works. I have a P35 board so I can't test myself so I asked if anyone here tried it.

On my DFI board the BIOS gives the option of which PCIe slot to initialize first, or you can basically turn either one of them "on" or "off".

I dont see why everyone is bagging this out. I almost had to put my main GPU in the second slot not long ago to make sure i got all my expansion cards in, although i found another way. I own an Asus P5B-Deluxe with a P965 chipset and it worked ok for me, but with a large exception

http://www.tomshardware.com/forum/249291-30-card

Checking out my POST there, i can tell you that my 7900GT worked perfectly well by itself in the PCI-e 1x slot not only did the machine post first go with it but it also ran games OK (although there was a noticable performance loss, for obvious reasons)

My answers

1) Yes
2) Yes
3) I dont see why not.

@jitpublisher
You own an ATI chipset from what I see in your configuration (I'm more interested in P35/X38/X48) but it's good to know that other chipsets offer this feature.

@chookman
Good to know chipsets are not picky about this. I'm not considering installing any graphics cards in PCI-E 1x slots just yet. EDIT : A brave mod indeed. I would have really considered the ZALMAN FB123 before putting the soldering iron to my board. The second thought would be to sell 8800GT and buy a 8800GTS.

I dont think the Zalman would have helped me... and the 8800GT i bought for the upgrade, but i dont see how using an 8800GTS would help

The GTS has a two slot cooler. Sticking with the stock cooler would free up the adjacent lower PCI slot. Mounting the Thermalright aftermarket cooler on it you'd be in the same situation as now.

The FB bracket would allow you to mount your fan(now on the Thermalright) directly above the expansion slots. It would likely cool less but free the slot covered by the fan.

PS:
I'm just thinking how I would solve your problem if I needed to. It would need to be tested and the results compared. Your sollution works for you so that's that.

My 650 has three modes, one x16 slot enabled, SLI enabled at x8, or independent x8 slots where one card will function as primary in either slot.

All good Andrius, thanks for the suggestions