Sound like you might have an alt issue. It could possibly be putting out too much voltage to the battery. Or the voltage regulator (which I believe is in the alt) could be bad. Easy way to check. Hook a digital multi meter to the battery. Should get about 14.5-14.9 volts. Will the issue happen if the tranns is in neutral?
1994 Mustang GT
Bought for $2200,Had 97K miles,New fuel tank,New driver front hub,New pass ball joint,New alt, New battery,New fog lights,New plastic bezel shifter,Fixed check engine light,New tires,Coolant flush,Magnaflow exhaust. Its starting to come together towards stock THEN I will make it go FAST!