You should stick with an A9P then as the o2 sensor harness is different from auto to 5spd. Most people have no clue about this. The o2 sensors will not work correctly and you will be stuck in open loop.
It could be a wiring issue as well, check Pin 1 on the ecu and make sure it is seeing 12 volts, if not it is a wiring issue. If it is getting 12 volts the computer might be toast.
Ya that base kit price does not come with a y-pipe or anything else. I have seen good #'s from those kits and most of the guys that own them seem to like them so IDK.