There's really not that many different ways to get more power out of the Lincoln AJ engine. I don't know just how deep you can program this car with the SCT software, but if you can alter displacement or the fuel/air and timing map then your options open up. You can put in a larger displacement AJ engine, put in a different engine altogether if the new engine is modified to use the AJ engine sensors, you can even put a turbocharger or supercharger on it provided you can decrease compression enough to actually make use of it with something less than Avgas. Even just changing the cams on the AJ engine isn't going to make enough of a difference to be really noticeable unless the computer can be altered to use the new cams effectively. But, if the SCT software just does fixed maps that they send you and won't let you tune it, then you're out of luck. Someone really interested in this might contact this Torrie fellow that's talked about on this board as being an LS tuner to find out what he can do along these lines. About the only other thing you might do is put in an engine with a different computer that does let you alter it (the infamous LS powered LS comes to mind) IF you either piggyback the LS computer onto the engine computer's outputs OR double up the sensors to keep the LS computer happy where the auxiliary systems are involved. Otherwise you get that other LS powered LS's same problems with the air conditioner and ABS not working. The LS computer is totally tunable using either Tunercat of EFI Live software, either of which is an excellent product. I use EFI Live on my Chevy products, and it does allow total tuning. I can do things that even the dealer can't do with it.
It's a lot of hard work, but if someone really, really wants it they can make it happen.