With the eaton on top the motor will get heat soaked eventually. Depends on a lot of factors though. You probably won't notice the 5-10hp loss at the level you're trying to get.
My car came with the Gen V so I can't speak to the added cost of that. But my Headers, Cam E85 build ran me about $2000 in parts, tools, etc. I did all the work myself, including shift kit on the trans and DHP tune by me. Doing your own work will save you money, if you can't, double that 2k easy.
I only got down to a 3.0 on E85 with 20* timing. Never liked how the 2.8 felt. Too little timing, too much KR.
IF E85 is available in your area go with it.