What exactly did you do to the water pump to determine that its working fine?
Water pump problems are not completely uncommon in the 3.5 I can think of a couple cases off the top of my head. The guy who had his pump fail in the middle of a road trip springs to mind.
Could be that your WP blades are shot to heck, or something like that.
Right now RockAuto has a limited supply of water pumps for 29.99 plus shipping.
If you want to order from RockAuto go to the last page of this thread:
http://www.fatwallet.com/forums/hot-deals/370308/ There you will find a discount code, its not much, but its better than nothing.
Im curious to know how you ran it without the thermostat in it as well, as its all one piece, and the thermostat itself didnt appear removable, but I could be mistaken.
If youre refusing to take it too a mechanic, then you dont have much of a choice but to start replacing things. People have had problems in the past with WPs, much moreso than radiators, couple that with the fact it was still overheating with the thermostat completely removed, sounds like a dying water pump to me.
At the very least you could pull your existing water pump off and see what it looks like, directions dont look terribly difficult, and its not like you have any coolant to lose since you filled up with water.