Transmission not shifting and acting as in neutral

I recently had the transmission rebuilt. This problem began occurring not too long after where the transmission will slip or shift poorly between the lower gears and now the solid check engine light is on. I noticed the problem seems to happen more frequently when I have the radio on. I am now wondering if it may be an electrical issue. I have a few electronic accessories I installed into the car such as an aftermarket radio and a sub-woofer with amp wired to the car battery. I am wondering if these things may be causing the cars electrical system to overload or making the electronic sensors in the transmission malfunction. When the transmission guy looked at it briefly again the last time he said the transmission seems fine with the fluid levels and of course the problem did not happen when he test drove it. When he originally did the rebuild he found that the negative battery cable was improperly grounded so he installed a new one. If it is an electrical issue could it be the alternator or the battery are being overloaded? Everything else with the car seems to be fine as of now.