I was wondering what ratios I could use,and where I could find them for a VLT diff? Also what ratio would you guys recommend for every day street use behind a 5 speed with 350-400hp?

The ratios out of any Borg Warner 78 series diff is interchangeable apart from the 2.77:1 ratio used in the Fords to my knowledge. For that amount of horsepower I would tend to think that a rebuilt VLT 4 pinion LSD would suffice as you start to look at Ford 9 inch differentials which are mainly for very high horsepower cars and cars with a huge torque output. Once you start going for the 9 inch the losses in horsepower increase and also you have to get the differential modified to fit under a Commodore which means it needs engineer certification and it costs a fortune to do. I know a mate of my brothers was crapping on telling us to fit a 9 inch underneath our Commodores telling us that he can get a Ford 9 inch for $200 when the reality is it costs more than ten times that much to do fit that differential into that car,he told us this when we were after a Borg Warner LSD centre for our cars.

I already have a 28 spline 4 pinion LSD with 3:45 but I would like 3.9's... So do I need to find a 28 spline 4 pinion lsd with 3.9 centre?or am I only after the gears out of any borg warner 78 series lsd? I know pintaras have 3.9's but they are 25 spline,could I use those?

Go the 3.9's. I just got a set put behind my Walkie and they are fantastic. I have been told to keep away from the Pintara gears though, better to buy brand new ones.