I would definitely be pulling the manifolds off, porting is basically pointless if you're using standard cams.
My grandpa has one on his smallport in an MG Magnette, and it works very well. Has so much more capability than a 4A-GE will ever need, as they're such a simple engine with so little sensors to run and manage. Any of the higher end ECU's will be able to get a similar result, like I said they are a very simple engine. No VVT, no variable lift etc.