I always looked at it as the more you do the less you have to do approach... then I look back at all of the bits I have fixed and what has been achieved. But never look too far past the next job at hand. That is what the list of jobs to do on the bench is for. Good work mate, keep at it as I think that the best part of the build is the build itself.
Brings a few questions first... how far back is the V6 set into the car? Depending on this will be how much work you need to do. When I put the v8 into the Ute my first consideration was cooling it and how I was going to set up the radiator then thermo fans and also the air. Once I had that worked out then I had the starting point on how far I would need to mount the engine. The shortened commodore diff will work nicely and then it depends on if you want to retain the hr front end or change that out as well. I would get in touch with your engineer if choice before starting though mate. The rules are different from state to state.
Having done a Ute and not a van (yet) would say the extra metal on the long roof wouldn’t count for too much and depending on what you are doing with the chassis, level with the tray would be a good start. I found the more I did to the floor the more weight I added so it became bottom heavy. But not too much so that I couldn’t turn it.
From memory I went 75 mm strip down the tubs and get 285’s in ok. So you may want to get the tyres on the rims to make sure of the tub size needed. Cheers