I'm going to fit spotted gum toe rails because of damage to one of the aluminium ones, I'll bolt it on but i would like an effective adhesive/sealant to bond it. Any recommendations on what would be the best stuff? I'll be using a fair bit because I don't want any moisture in there between the glass and timber.

3M 5200

I've had excellent results with Simpsons, black or white

Why not epoxy ?

That was a thought but I may need some flexibility I don't know, it's timber to glass and bolted through

Timber to glass, you def need some flexibility. Epoxy would probably be too brittle in that application.

None of my business but what is the yacht type/model and alum toerail section type (oem, model/type) and the specific damage to the alum toerail? And the damage to the yacht hull to deck joint?

We had damage to one toerail in 2 locations (9.3m 2tonne racer cruiser yacht) when driven onto wharf poles in a mongrel westerly which went from 20kts to 45kt in a few seconds on an infamous day on the west Sydney harbour. The whole harbour got flattened - 16ft skiffs were cartwheeling out the heads.........we got off the piles/wharf and back to the mooring and looked at the damage for a few seasons and finally took that side whole toerail off and back to land and got the kinks out very well. Not a 5min job and not as new but hard to notice now.

If you want to post photos I can compare to the damage we had - will respond with photos if I can find them and methods we used - overall bending of the section back to the original curvature over formers, and local panel beating of the local section dents also using formers and short hardwood pieces. Aluminium in general is not as easy to persuade bends and kinks out as 304 or 316 stainless steel due to its different material properties.

r13 it's a Sunbird 25 M/S that was storm damaged, some gouging in the glass on the port bow from another boat hitting it (not to bad just needs filling and sanding ect) the toe rail is actually missing altogether leaving just the screw holes, I doubt I could find another one to match so I think changing to timber is the only option.
I'm just doing the repairs and paint then selling it because I got it cheap and it has a good engine, sails and the rest is in good order just needs a tidy up.