Your #'s aren't bad...i've seen 99-04 auto's do 210-220...and dyno's are just a tuning tool thats it.
What type of Dyno?
What type of Dyno?
one of my buddies put down 204 in his 98GT with BBK shory headers, x pipe and a cold air thru a 5 speed...
its also possible that your tranny or tq converter is worn and sucking power... its also possible that your rings could be worn and your not getting full compression...
My compression is fine, we had to do a compression test when installing the cams/manifold to rule that out as a reason for it running so crappy (turned out to be 2 plug wires were mixed up).
Did your friends 98GT have PI cams/manifold/(heads) too? If not I find it hard to believe a NPI mustang put down 204 to the wheels with just headers, xpipe and cold air...
Also Hi-Flow cats only take about 2HP away so O/R vs Hi Flow isn't TOO big of a difference.
Why is that? A 5 sp will put down 190rwhp stock...so 14hp increase isn't that much especially considering we generally gain @ 10hp from ditching our stock mid pipes.
You have an auto and they will read up to 10% less then a 5 sp...
Throw a nice TC and do the Jmod and you won't have a problem with the extra 10-15hp a manual will dyno.
thats 215FWHP W/15% drivetrain loss. 
have you checked it since the wire swap?