I've just fought through my electronics on an e40d rebuild. My hard shifts appear to have been caused by a $10 part and corrosion. There are three connectors on my tranny: VSS (which was my issue, the gear on the end of it specifically), The connector on the passenger side showed a lot of bare copper on the harness side and was replaced and the connector on the linkage wasn't much better. I found tons of corrosion in the connectors where the trans harness connects to the main harness under the master cylinder. I also found my harness from the tach sensor and fipl (tps) to have a rub through on the alternator as it was no longer attached above everything. This caused slight fluctuations in the tach or the convertor was locking and unlocking. I also cleaned my brain connectors (it seems to have a good seal and wasn't necessary) and adjusted the fipl (look in the tech section). From what I understand the fipl, tach, and VSS are the only sensors the brain uses to control the trans. There are some checks I found while searching the board on my issue, but didn't apply since my tranny was fresh. Things like checking inside the wire connections on the tranny for fluid, checking line pressure.... I'd inspect the connections/harness on the trans, and the fipl/tach. I'd clean the tranny harness to main harness connection - battery disconnect if you use metal on the females. Then I'd run it and check the codes. Still problematic - move on to line pressure and inspecting the connectors in the tranny and by that time some of these smart guys will chime in. Oh my rebuilder said, I would only be messing up the trans while I was testing it, if it was messing up in reverse....
