Sounds like you have a signal fault as in data being lost and so MPU locks. It COULD be 40 pin connector, but pulling this out is a lot of work and if not necessary, its tempting to avoid it.
You can retension the female side with a small screwdriver and as sacriligious as this sounds a light spray of CFC on the male. Put back in place and if symptoms are no longer then this is your fault area. Of course it doesnt fix it, but it does determine the fault. if its not here, then spray connectors with electronic cleaning spray to clean up.
make sure also that signals from PIA chips are above 3V. Ive had PIA gradually die on me and under this voltage is not seen as logic... game will just freeze due to low logic signal.
And yes - as nino states... 5V logic cap... check for RIPPLE!!!!
