You will not need to make it "manual", all you need to do is remove all of the transmission related codes that come up after you get going with it... I can provide you some manual base files to look at for that stuff.
When tuning a car like this, you want to keep it simple, as you have not change all that much in the eyes of the ecu.
One concern with manual swaps is the idle control settings are much different, but usually if you have a speed sensor hooked up and calibrated correctly it will work fine without adjustments. I can advise you on how to solve issues if you have no VSS available.
