What order did you try fixing your overheating problems in? If you started with the 160* thermostat which is probably the easiest thing to do, that may be part of your problem. If it's essentially open all of the time, the coolant isn't in the radiator long enough to cool off.
Your starting problem sounds a lot like a leaking fuel pressure regulator. It could also be a bad PCV valve. I had a Paxton FPR and used octane boost. This caused the diaphragm to deteriorate and started leaking fuel out of the vacuum port into the intake. The symptoms were long starts and backfiring.
With 30# injectors (They're good for at least 450 hp), there's no need for you to have an adjustable regulator. I would just get a stock replacement and see how it runs. A stock replacement isn't that expensive. If you still have the problem, I would then perform a leakdown test. You may have a leaky injector.
Have you pulled any codes from your computer? Running a cylinder balance test may also be useful.
Just some thoughts.
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351W 89 Mustang GT Convertible