No reason to go 5.4, I'd go with a Teksid block 4.6 to drop almost 100lbs off the nose and you can do 800hp with a 2V or 4V either one will get there without much effort. TFS 2V heads cost about the same as a set of C heads totally gone through and there is less valvetrain and they are lighter. But that's up to you as well. If you ever want to go over 4 figures for power numbers the 4V is the way to go.
As far as the On3 kit. Its a good base kit but I would not run their turbo/wg/bov for a big money build like this. The tubing/headers do fit very well though. Only big issue is it is designed around Unauthorized Product Reproduction (UPR)'s k member which is a VERY good drag K member but if you want to handle its no better than stock. On the other hand if you were to buy the BEST turbo kit out there (Hellion) you can run a Maximum Motorsports K member/front setup as they have a K member specifically modified for Hellion's stuff .
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.