Keith.
My usual proceedure is to place the body on the chassis,drill and cut all holes,fit bulkhead panels,fit loom,fit pedal box,fit column bush and just about anything else that is in the engine bay including the bonnet,remove bonnet,remove body.And then to the chassis fit axles,fit brake pipes and battery lead and fuel line,fit engine and box,fit radiator and then remove,sort out headers using templates for footwell,remove headers,re fit body and fix it down.Fit wheels,fit doors,fit exhaust and so on...
My proceedure will probably vary from yours as all my builds are done with all the parts "on site" from the word go,but you get the general idea.
This proceedure works with small block engines,but a big block may need to be removed from the chassis and re fitted after the body has been fitted.
Any probs,give me a call.My contact details are on my website
www.v8cobra.co.uk
Advise is free,i only charge when i get my hands dirty.