aftermarket ecu

[velj1]

hey guys, recently we have finished out cobra! and thank god for that,
we have put on a mass-flo efi intake system, and cant get the car running right, its been a while and would have though the ecu (a9l) would have tuned its self by now over 1000kms of driving
we have spoken to a few people with aftermarket ecu's in there cobras and are leaning down that path to.
what i am wondering is,
what have people put into there cars?
what are some decent brands? but dont want to break the bank
how much would i be looking at spending?
car has a au wiring loom inside running a mustang a9l ecu manual 5 speed!

thanks
daniel
PS: where could i start a thread about our car from start to now, like a car journal?
thats the finished product