Hi David,
Really nice work! Having been down the rabbit hole of body fitment several times now with KVA, GTD, CAV, RCR and MDA I can confirm there will be many hours chasing the optimum alignment of all the panels.
The key is to make sure the roof spider and windshield are square on the car, then put the doors on. Don't even think about the front and rear clips until the roof and doors are happy.
Then set the front and rear clips on and adjust for gap to the roof spider and cowl. Be prepared to change the sitting height of the roof spider at the sill boxes or windshield surround as it rests on the top of the cowl (keeping an eye on door gaps). Remember to give yourself some allowance for the thickness of whatever you're closing off the cowl with as that will raise the roof.
Then put the sill box cover moldings on and see where the overall length of the total body fit between the wheel arches and the sill box ends line up. It takes a lot of fiddling but it will all work out. You may have to play with the front and rear pivots to get the best fit horizontally along the sill box too.
Make sure you have about 1/8 inch clearance between the front and rear clips, doors and roof spider above the sill box moldings. Once the overall alignment is at it's best, then you can fit the latches and catches and pins.
This process should give you the best body fit with the least amount of rattles and squeaks on the road.
Cheers
Ian