Your plan so far is pretty sound however a few ideas to throw out......
Adhesive between the original glass and junkyard gasket: As originally built that gasket is supposed to be part of the glass---its what we call and encapsulated assembly, they're bonded together. When new glass is installed during the original build or replacement glass used that assembly is simply bolted to the body using butyl tape in between as you have already discovered. Since you were able to separate them that's great as it eliminates on part of the fabricating solid metal glass replacement parts. (I'd be curious what tools you used separating them---might be able to adapt that myself.
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FWIW I have/had a slightly different approach in mind regarding the gasket and metal. It involved basically building my own gasket of sufficient thickness to allow installation of a single sheet of 16 gauge steel that would be flush with the body. The how-to of that is another story for another time perhaps.
I'd not use the spanner head screws you show as the tools used to hold those while being tightened are very fragile and cannot hold sufficient torque without breaking as you're clamping the metal/gasket assembly to the body. I'd look for a truss-head bolt that is similar to a carriage bolt but instead of a square projection under the head there are two "tangs" in place of that part---these will dig into the metal enough to allow enough torque to seal your assembly to the body.
(I'll look for those bolts I mention and update this thread when I have more info about them.)
Your question what goes between the gasket and the metal would be silicone adhesive/sealant, stuff that's available from Lowe's/Home Depot for exterior grade use. GE makes a Type III I like, it's less than $6 a 10 ounce caulking tube. Its easy to work with and does a great job while being able to be removed if that need ever arises.
I honestly like your approach to all this JVan, hoping I'm helping rather than mucking up your process.