69 RoadRunner. What are the options for sealing the gap along the top of the fender and fenderwell to mimic the factory results?

White Dum dum strips work well.
Or liquid butyl in a caulking tube from the hardware store.
You don't want to use anything that will glue the fender on like seam sealer.
I prefer to put the fenders on without any, then once everything is final fit, I'll squeeze some in from the underside before undercoating. It has the added benefit of not letting the undercoat spray through the gaps and make a mess in the engine bay.

I used a 3M two part foam, but that stuff sets up super fast so you better have a buddy help you. Looks super.

They do make sealing foams and body adhesives that grow substantially when they cure so be sure to avoid those. I had a couple of the daubs of hood sealant between the hood skin and the hood brace come unglued and the product I bought to re-attach those was the kind that had minimal expansion properties. If in doubt tell the body shop supply place what your doing, or call 3M and ask what they recommend.