Since this is a more permanent install of camper to vehicle, I'd at least recommend a rubber strip between the new camper frame and the top. To hold them together and aid sealing, screws up from the bottom through the top and into the aluminum would lock them together. After that I'd still seal the seam with a flexible caulk to help keep wind driven rain (at speed driving) from being pushed into the joint between the top and camper.
As far as filling the area between the top and the camper with spray foam isn't a bad idea, but I would add some exterior board or skin to cover and protect the foam. This would give an added aerodynamic benefit by keeping the air from going under the cab over section and directly into a flat wall of the front of the camper. To me it might be a bigger challenge to make that look aesthetically pleasing or nice.
I've seen some FWC campers on early K5's that were full convertibles and lacked any solid frame around the door windows. Where most ended up cutting the front "cab" section of a factory fiberglass top I've seen one in a junkyard that they used no section of the top at all. They framed up the area that the door glass to seal to with wood and filled in the gaps to the camper with foam. Needless to say the area looked poorly done and lacked sealing to the glass at all. It just wasn't executed well at all.
I went back through my collection of K5/FWC photos and found one that shows what I described above. No Blazer top section was used and the camper section over the cab was used to make the interior roof section of the cab of the truck. It just looks cobbled and poorly executed.