I'm not sure if this will answer your questions but it might help. Here is my problem and planned solution.
I have a Asus A8n-sli, 939 socket. I'm planning to use an FX-55 processor if I ever get it. x*(^%.
My BigWater (BW) issues are similar to yours, 2 screws, Mother board (MB) plate on bottom, etc. If you email me, I can send pics.
Sounds like my MB has the same configuration. I removed the stock plastic bracket and plate. The plate comes off my MB and I pretty sure it is removable from yours. It needs an insulator to separate it from the MB. In addition, there should be some Surface Mount (SM) components under the plate, just under the 939. To make matters worse, these components interfere with the ThermalTake (TK) H bracket. You DO NOT want to put pressure on these SMs.
Here is what I'm planning to do:
1) Remove the stock, plastic bracket and plate.
2) Drill the existing screws holes out in the stock PLATE so the 2" TK screw will slide through, say 0.125 or 1/8". Do not damage the clear insulator or get metal shavings on it.
3) Notch out the plastic bracket to clear the BW water block.
4) Reinstall the PLATE and plastic bracket using TK screws from the bottom of the MB.
5) Use the TK washer and nut to secure the stock assembly with 2 screws. Now you have the threaded portion of the TK screws sticking straight up in the air. (when the MB is upright)
6) Install the CPU with thermal grease.
7) Put the BW water block on to and secure it using the TK "H" bracket. Once you snug it up, use a second
nut to lock it in. Not too tight!!!!! Use the second nut to lock it so vibration will not make it loose.
This operation is somewhat reversible, you could go back to a stock config. You would just have to
remove the whole 9 yards and cut the TK screws to exact length, Reinstall then you could use a stock
heat sink. DO NOT EVER EVER EVER drill holes in the MB.
USE ESD PROTECTION