95 Dodge Intrepid Running issues

We recently bought a 95 Dodge Intrepid for my son and it ran like a dream. Then the check engine light came on and we stopped and notice the radiator had a crack in it. We took it in to get it changed. We forgot to give them the key fob to turn off the car alarm and they accidentally set it off. They disconnected the battery to shut it off. Ever since then the car has ran terrible. It just started running rough at startup. If he turned it off and restarted it, sometimes it seems to run smooth again. Now it just runs terrible and has no power. We took it back in and they changed the O2 sensor, crank shaft sensor, Cam shaft sensor, checked the coil, plugs, and fuel pressure. He said the fuel pressure was a little high. Can anyone help us? The next thing he wants to change is the module and that is around $300. Are we overlooking something? Here are the specs on the car: 1995 Dodge Intrepid, 3.5 V6, R16 tires.
Thanks for your help!!!

what module that costs 300 bucks? I'd find another repair centre it sounds like the one you're going to is clueless! Has anyone verified the timing belt hasn't slipped, Checked fuel pressure, egr valve, fuel trims, have they used the correct parts?

Buying it from Napa. That is what they quoted us. It is the "brain module". Not sure what it is officially called (located under the air filter) The mechanic did check the compression (good), fuel pressure (good), checked injector ohms (good), checked injector spray patterns (good) and changed the coil and wire. Mechanic is very good... hasn't charged us a cent because it still isn't fixed.

Just because he hasn't charged you doesn't make him any good. Removing working parts and installing parts of questionable quality in an attempt to get lucky through shotgun diagnosis is doing no one any favours. Is he buying all these new parts or changing them for you for free becasue none of them fix it? If this started right after the battery was disconnectted has anyone gone back and looked for loose connectiion or poor cables at the battery? did it overheat ever before the rad was replaced. It's not a complex car and like I said it sounds like your guy with tools is clueless. an injector ohm test is useless! Has he verifed the timing belt is still synced? Fuel pressure on a road test? exhaust backpressure?