I will be putting a AU motor (slightly worked) into a ef or el(havent purchased the car yet, but i want that shape) and i will be getting a manual conversion so i will almost certainly have to purchase a manual ecu (seeing as the falcon i will buy will be auto)

So im just wondering if it is ok to use a ef/el manual ecu to run the au motor, or do i need a au ecu?

thanks and i hope i havent confused you to much lol

The EF ECU has 104 pins and the EL has 60 and do not interchange. You would have to buy, if you can find one, a manual ECU to suit whichever model car you get. This is the best way, however due to their scarcity, most who do the conversion trick the auto ecu into allowing the manual to operate. This is good but not perfect, use the search function to locate threads outlining this procedure. Try searching for "auto to manual" or "manual conversion" and read the threads.
First read the 'stickies' at the top of this forum on engine changes and you'll find some leads there.
Cheers
Paul