Richard, being the genius he is (I owed you one ), has given you the best route. Sinking the windshield takes some logistics as there are other systems under the cowl that need to be modified. Not sure about the glass you use there, our methods, on later model cars, are based on a laminated windshield, and tempered side glass.

As you surmised the side glass is relatively easy. Rather than the plastic for the flat pieces, which scratches easily, folks here will transfer the pattern to flat, laminated glass, which is what the older cars came with. Rather than MDF, we use a material that's called Masonite, or tempered hardboard. You likely have the same stuff, but perhaps under a different nomenclature. Same stuff that peg board is made of.

The curved glass is a different matter. Some grind away the unnecessary part, others find an experienced glass guy who scores the new edge and breaks it off, frequently breaking the part to be saved. It's not uncommon to "kill" several windshields before getting one that survives. The back glass is probably tempered and would work better sunk in, or you could use the perspex if you can live with the potential scratches. The old glass would be used as a pattern to mold the perspex over for curvature, then cut for heighth and width.