The results are in!
4th Gear was destroyed due to a lack of lubrication. They tell me that one of the FMIC pipes was pushing against the trans cooler hose and squashed it to the point it was severely restricting flow. Lucky for me that they also fitted the Fabwitz front mount intercooler and pipework.
Its good to see a shop that stand's by its work ethic and accepted full responsibility for the repairs. They said they'll do their best to get it done by the end of the week. Thats good enough for me, and I'm a happy camper again.
So best to keep this in mind for those mounting their own FMIC. Make sure none of the trans lines are getting squashed! It's an unusual one and not something they've had to deal with before. Hopefully this will be the end of my troubles with the auto.