If flexing is hardening and breaking the welds, then I don't think glue would be a long lasting solution. Even if you can get the 2000+ psi specs they claim (done under clean lab conditions) you must remember that in a glue joint such as you propose, all of the stress is concentrated in the edge of the glue line and can be very high. You need to consider the peel strength of the joint as limiting, not area x adhesion. If you try glue, I would try one of the varieties of Plexus, it bonds better to metals and has very high elongation compared to any epoxy. I think it would be difficult to do through an access port.

Welding the baffles in would be preferable, and some attention might be paid to the design of the baffle and joint to mitigate flexing and spread the load if possible. Probably requires tank removal which can be very difficult in some boats.

If that isn't practical, I would look into baffling with foam. Find an inert very open foam or fiber mat and fill the tank with it through the access hole. They make this stuff specifically for race car and aircraft tanks, don't know that I have seen anything specifically for water, it looks sort of like a very coarse Scotchbrite pad. It can be removed for cleaning and is actually a much more effective baffle than even a few solid baffles. The kind of material I am talking about will only reduce the capacity of the tank by a couple of percent.

For example: http://www.atlltd.com/blue-baffle-foam-diesel-water-methanol-use.html

That's the first hit on google "foam water tank baffle" and happens to be in England but you can search.