Rob - what you can't get done today will be happily waiting for you tomorrow. Your Cyclone is one of the best shown here, no need to rush. Give yourself time to heal and recover.
I think I'll cut the windows off the piece holding them together and file as needed to install them separately. If I have to make and glue small clips inside the body to hold them in place I'll do that and make a shim from sheet styrene to fill the gap between hood and bottom edge of the windshield. When I time trialed the chassis with bare body a few weeks ago it ranked in the middle of the cars it will run against in my Muscle Car Stocks class and I want to see how it does in actual races.
Regarding my 2nd Cyclone, despite issues with the first car I'm imaging doing a version of this tricolor scheme on the next one.

I'll simplify the painting a bit by doing the front half in blue and the rear half in red, then print white ovals with '48' in them for decals on the doors and roof. If the paint seam between front and rear colors isn't crisp it'll be covered by the white decals. Once again, this is going to be a racer not a shelf queen so I'm only concerned about making it a tribute car for James Hylton that will be competitive in the Muscle Car Stocks series.