Engine misfire during use

Hey, recently I bought an 04 mustang with the 3.9 v6. It had been parked for about two years so it needed quite a bit of work done to it. I won't talk much about the PCM issue that I had, but once the car started I ended up running into an issue that pretty much made it undrivable. When I would drive it, the engine would eventually hesitate then decelerate and finally the rpms would dip, causing the engine to shake and shut off. The only way to drive it again would be to turn it off and then start it. I'm going to describe it a little further so that way I can help those having similar problems.

My car would decelerate and shake until it shut off only when I:
1. Drove it in the day (also at night, but these were rarer) under normal operating temp
2. Punched it when trying to overtake someone
3. Drove up hills or any where it would have greater load
4. Anytime I would go above 3000 rpm

I changed the coil pack and it turned it into a different car. Since I did that, it no longer acts up like this but I occasionally get that hesitation and jerky ride until I let off the throttle and let it coast. Usually fixes it right up so I can keep on driving. I'm assuming it's still misfiring. Any areas I can check up to stop it from misfiring? I've been thinking of checking the fuel injectors now since I've never inspected it since I bought it. Any help would be appreciated. Thanks