I have a 95 3.8 with cold air intake, ford racing H pipe (no cats) and magnaflow mufflers and had the same problems you do.
Here are some things to look for. Also is your car shooting any check engine
(ODB) codes? Alot of times if you are running a catless exhaust and dont have MIL eliminators it will shoot a check engine code but then again I've seen mustangs that dont shoot the code.
-Check for vacuum leaks your system can detects a leak as small as 1mm in size. Yes this even means check the security of your oil cap. check all hoses that attach to the intake manifold and all hoses that run downstream the MAF and upstream of the 02 sensors.
-I saw you already cleaned the MAF but that helped me alot I just took it off and sprayed some brake cleaner all over it and some on the sensor itself and repeated it about three times.
-Take your CAI off to get to the throttle body and inspect it and then manually open it and see how much black residue or how much dirt is on it and you can take some electronics cleaner and spray it down but dont scrub hard the TB's have a special coating on them that you dont want to take off but be sure to get everything cleaned evenly.
-I also had an 02 sensor go bad and that took some power away from me as well.