Wouldn't surprise me if you are up against the Programming Not Finished flag problem. (Although one would think that APR would know how to handle it.) If flashing a stock 551 AA as you suggest doesn't work (there's one in the Original ECU Files section), modify a 551 R to suit (match the 551 AA or better) and run that. Or just run the R; at least you'll get your car back.
Can't remember which one it was, but the only structural difference I noticed when comparing AA and R was one not-terribly-important parameter that is a scalar in the R and a table in the AA. There are some slight timing differences (+/- 3* in a very, very few areas), and of course the different LDRXN. Probably other differences (obviously, otherwise we wouldn't have this problem) but other than the LDRXN they aren't noticeable on the road.
edit: Ah, crap. never mind. Thought I found a difference between R and S/AA EGT scaling, but nope, too just had too many things open in OLS and Tunerpro at once.