I'm in the middle of doing this to my canoe right now.

A few tips:

Have all your repair materials on hand before you start. Once you get the old glass off you'll want to reglass it as soon as possible. Make replacement gunwales in advance, copying dimensions from the originals.

I let mine sit outside through some humid weather (and some rain leaked under thre tarp) and the wood swelled. Then I had to wait several months until I could get it inide before it dried out and things shrank back into shape.

Measure the beam at several points before playing with the gunwales.

Usually the outer and inner gunwales are connected with screws or bolts. If you didn't use glue or epoxy in addition, then just remove the fasteners and the gunwale will come off. If you did glue it on, check for any fasteners before planing into them. Careful use of a sabresaw will remove most of the gunwale. Plane down the rest until you are nearly through. When the remaining wood is less than 1/16th of an inch thick, your heat gun should be able to soften the underlying glass and resin, and you can peel off the whole mess at one time .

Problem is, your thwarts and seats are probably connected to the inner gunwale--so when the outer one is removed, the inner one lets go, too. With gunwales and thwarts gone the hull springs out of shape.

You might want to try doing a little more than half the boat at a time. Start from the keel line and strip the old glass about 4 inches to the left of the keel, and all the way to the gunwale on the right side. When you reglass it, you overlap the keel area, and have it double-thick for some abrasion protection.

Go easy with sanding into any glass. Wear breathing protection. You don't want that junk in your lungs.

Good luck with your project. You'll be amazed at how thick some of the glass you remove will be.

PGJ