I looked at Evilution's button bank info again and he mentioned that the switches (except for the end ones) are momentary switches.
I took a multimeter to my button bank and confirmed that the switches are momentary closed switches and not momentary open switches like the discussions about transistors would leave you to believe.
After re-looking at Cubefx's mods I think I found the problem. You need to disconnect the "hot" wire from the wiring harness. The garage remote should be connected instead of the hot wire, not with it. For example, in Cubefx's mod, you need to snip the blue wire (and cap it) and solder the red wire to it. Otherwise the car will supply 12V to your remote and depending of how the remote is wired, you could get a current flow through the remote. Snipping the wire let's you use the switch isolated from the car's 12V circuit.
Important note: you don't want to snip the brown wire since all your buttons depend on that for ground.
Finally, I found another good place for the remote. I put mine under the cover that you remove to get to the radio. There's plenty of room and the remote isn't buried down in the metal part of the car. I think it will improve the range.
Hopefully, I didn't miss anything- I'll let you know if I end up with the same battery problem. Good luck and thanks to Evilution and Cubefx for paving the way for the rest of us.