I think the answer to your original questions are pretty clear - a Mazda MX5 monocoque does include not only the windscreen frame but also the glass. It is bonded in, not sat in loose rubber so it becomes a structural component. The second issue is whether its just rules or is it actually a real safety issue. Personally I wouldn't want to cut into the Mazda and expect it not to be compromised. They are designed down to the tiniest gram that can be shaved off and still be safe - there's no room for error.
There are lots of unfinished Lotus seven-style kit cars on eBay and even lots that have been registered but are in need of work. You'll find designs and plans to draw from everywhere on the net.
Have you thought of a TVR? A rolling chassis pops up sometimes and will give you a modern separate chassis to build from with registration.
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