not charging properly

OK, OP, thanks. When the car dies and only cranks, is the hard discharge seen on the ammeter at that time too?

If this problem is always associated with the brake pedal being pushed, then my first thoughts are similar to those above: I would first suspect that some part of the harness has chafed against the harness and is shorting or is being pinched by the pedal and/or rod. I would crawl under the dash and look very carefully at the harness all over in the area around the steering column, brake pedal and rod, etc.

Unfortunately, if the PO did other wiring mods to the charging circuit at the time that he wired past the bulkhead connector, then this is may be hard to diagnose over the internet. The ammeter going to D normally shows a hard discharge of the battery. Moving the point where the alternator's large output wire connects to the rest of the car can change how the ammeter behaves and make its indications non-standard, btu enve with most charging system mods, it shows a short or near short somewhere in the dash area.

You need to not mess around and find this because if it is a short like it sounds, it can cause a fire. I would not leave the battery connected while the car is sitting.