289 Engine issue when put into gear.

Well after selling my 79 mustang back in 2000 We have finally acquired a 1965 mustang. We have had it about a week and a few days ago it the 289 "A" code, seems to run rough once its put into gear. It seems to idle just fine. I recently replaced the battery, alternator and voltage regulator along with spark plugs cap and rotor. I've also noticed wiring issues when I just up and lost power a few days ago and found cleaning off the connections at the starter solenoid solved the issue and restored power. When it is put into gear it acts like it is struggling to keep turning the engine, when the gas peddel is depressed it run just fine. It seems like the engine was recently gone though, starts great, dose not burn oil, sets you back in the seat when you get on the gas. Any ideas what could be possible contributiors to the issue or where I should start to try and find possible causes. Also a few days after replacing the regualtor and alternator the alt light tends to blink on and off until you get on the gas, then it stays off until a stop light or something.

Thanks,

Knight rider
1965 Mustang "A" code 289
1966 F-250 352 V8 Custom Cab / Camper Special
1958 Mercury Monterey MEL 383 V8

Thanks for the info, I'll check the modulator. and see if that is the issue, It was converted to a pentronix electornic ignition before I purchased it. It has been ideling fine until a few days ago. Makes sense about the alt light. TIme to pull out the chilton from 1965

Thanks for your input I appriciate it!!

Knight rider
1965 Mustang "A" code 289
1966 F-250 352 V8 Custom Cab / Camper Special
1958 Mercury Monterey MEL 383 V8