mmm, its a big job, from what ive experienced with doing a HQ 1tonner for my SISTER, lol and half way through a VH sedan, looking at a blown 308, hopefully 350!
be prepared to spend some cash $$$$$
this is the order i would do it in if i was to start again now..
basically get all your body work sorted out, if your doing it yourself - bitch of a job, involves lots of sanding lol, id probly just pay a good panelbeater to do it, if i had the cash, if not its totally do-able, get all the prep work done and into primer than if your going 2pac paint, look to hire a booth, the dollars spent here will pay off in the end, no bugs or dirt in the clear coat!
then look at either the engine / driveline side of things, its not just the motor you would need to consider, wiring, gearbox, clutch/torque converter, tailshaft, diff, brakes, suspension, radiator, i know i wouldnt be spending money on a crate engine without knowing the rest of the deal is going hold up to the stress of the new power..
and then get it assembled being careful around the body work, alternatively you can do it in the reverse order, do paint last, i just found it makes the engine bay alot easier to do with nothing in it.. and i havent scratched any of the paint on the outside of the car, but still need to paint the engine bay, prick!!
save the interior till last itl save having to pull it in and out while you do the rest of the body work, its heaps of work, and time, but in the end itl be worth it!!
any smaller details i can help you with just ask! hope this has enlightened you a little bit!!
take it easy bud..