MPEFI is the correct choice. It will not cost you $11,000.
Use one of the excellent Plug and play systems from
DIY AutoTune <= clickable.
If you are n/a like most of the Cobra's then you want the 99-04 New Edge Mustang controller. Get the wiring harness out of a salvage yard. If you are supercharged get the 03/04 SVT Cobra ECU. Same comments on the engine harness.
If the harness is too difficult to come by get the
MS3Pro EVO with harness and trim the harness wires to fit your installation.
The MS3Pro systems will work with just about anyone's sensors. Many are preprogrammed others you can easily add.
You will need a set of injectors, fuel rails, electric fuel pumps a return style fuel pressure regulator and some motivation. You will probably easily come in under $4K.
Go to
Calibrated Success navigate to the DVD section and get their Advanced Tuning Series DVDs on tuning. Alternatively there are other very good training programs available from sources like
High Performance Academy
Ed