Manual M44 is a great option. I repowered my 1996 316i compact manual with a M44 engine and its great fun to drive. Really pulls well off the bottom and reasonably economical at around 8-9 ltr to 100 k. You cant go wrong!
The motor I bought was from auto so a live wire to EWS unit was needed to activate the Park disabler. That might be something you may need to consider if the wiring from the auto gearshift is removed or maybe its just a switch you can jam on. You will also need to leave the automatic control unit in place, if its removed the rev limit will be set to 5500 rpm.
Don't need to worry about the plugs into the auto transmission leave them tied up out of the way.
The Reverse light switch may need to be wired in to suit the manual.
You wont be disappointed.....I would definately improve the suspension though
