I'm Steve Smith.
I make CPES, and as a product manufacturer I cannot post on the Forum, since commercial use or self-promotion is not permitted by forum rules, and my very name is self-promotion due to my business. I am therefore replying to you directly.
3M makes 4200 and 5200, and both are available in black or white. UV resistance of either will be adequate, although black will soak up more heat from sunlight. More heating means more physical expansion of the elastomer, and thus more stress on the glass and wood.
Wood trim on the outside, around the windshield edge, blocking the UV from going thru the glass and attacking the sealant-glass bond,, is recommended and will give a nice appearance.
The wood needs to be primed with Clear Penetrating Epoxy Sealer(tm), also known as CPES(tm). Allow it to dry at least a day, if the wood is sound, or several days if the wood was somewhat deteriorated and soaked up quite a bit of CPES. The solvents should be largely dissipated before applying filers or sealants.
The glass needs to be cleaned with an alkaline solution, as pH above roughly ten dissolves a few layers of molecules of glass, and you then have a chemically clean surface which water will sheet off of. A strong solution of Cascade or similar automatic dishwasher detergent
will do. Abrasive cleaners are optional, if for instance silicone
sealants were used.
Use 4200, as it is a lower-modulus sealant than 5200 and for a given amount of inevitable structural movement it will develop less stress on the adhesive bonds.
4200 and 5200 are isocyanate-terminated urethane sealants, and should
bond just fine to chemically clean glass. They also will bond very
well to my CPES, even if fully cured and a month old.
As for joint design, put in some wood-or-whatever spacers, and pull them out before the sealant is fully set, and backfill those holes. The ideal joint design has the glass floating in a bed of elastomer on all sides. A reasonable elastomer thickness in your application is an eighth to three-sixteenths of an inch, if using 4200. I am on the Chris-Craft list if you need more info.