Audi-cycle

Alright, so let me start at the beginning: I have a '98 Audi A4, 2.8 30v. Back about 1-2 years ago the old engine died, and my stepdad found a new one for me to buy, and we both installed it in the car. However, it was out of a 99 or 98 audi A6 instead an a4, and it was automatic unlike my car. The only differences I am aware of between the 2 is the throttle body (I know that now, hah) and the bushing (which is gone, not a thing anymore in my engine, obviously). Now, when we first put the engine in, we had an issue with the TB not working/reprogramming properly. Eventually it ran well again, and has been until about a month ago.

All of a sudden, the throttle started going nuts and the check engine light came on. Figure'd I'd just find a new one. Well... I can not for the life of me remember if the first throttle (lets call it tb1), came off the a4 motor or the a6. Anyways, i found a tb at the junkyard also off a 99 a6 2.8, however, I was not the one who removed it and have no idea if it was an auto or manual. Now, this one has the low pressure bypass valves on the bottom of it (we're calling this junkyard throttle tb2). Anyways, i go to install it, see that tb1 doesnt have the low bypass, and figure **** it, might as well try it. Well, it didnt want to program either, but its acting much better than tb1. Tb1 tried to drop down to 300 rpms and back up at idle, but was fine while driving ( of course this was after cleaning it, and hardly ever driving it since I take my motorcycle everywhere to save gas and mileage on my baby). tb2 drops and wiggles quite a bit during idle, but doesn't drop as low - more like 5-600 and up. It is acting very very similar to how tb1 acted when i first put the motor in, still no problem while accelerating. But, tb2 won't reprogram (rosstech using 098 as the motor).

So, my question is - would it matter if the throttle was auto or manual, low by pass or not, and am I using the correct number in the rosstech system? Since the motor in it now is auto, would that make any difference? I would think not, I would think the manual tb is the best choice. I am a poor college kid and don't want to buy the $280 tb basically. Should I return the tb i put in to the junkyard and try to find another? (it is pretty easy to get in and out), or should I try and see if I can reprogram it still? Any help is super appreciated!