The TPS is your problem. You must purchase the re-designed model with the TB or you will have running problems. You can check www.rockauto.com
, and they had some made by Doorman IIRC, or you can check with Village Ford
, our OEM parts supplier who gives us major discounts on Ford parts.
You won't have to worry about installing the TPS wrong because it comes installed on the TB. You are correct though, the TPS must be fitted to the shaft, not the screw holes. Typically it is tilted slightly towards the air intake, and it should slide on flush without force. If it doesn't fit flush, then you don't have it lined up properly. Then you rotate it back to line the screw holes up.
edit: Rock Auto doesn't sell the TB you need. You might end up having to go to a junkyard, but there is no telling if the part you get is working or not.