Look for Sven Pruett's How to Build and Modify Ford 60 Degrees V-6 Engines.
http://www.amazon.com/Degrees-Engin...ional-Powerpro/dp/0879389141/?tag=959media-20
Not cheap, but a lot of useful performance info. Might be able to find someone willing to sell for cheaper, but it is a rare book.
Injection is entirely possible on any engine. I would try to do a multi-port setup for fun if I were in your shoes, would need a 2.8L intake to play around with, but going cfi and following the instructions on that link would prevent you from having to think about it too hard.
Lowering - DJM lowering i-beams and rear flip kit.