The forward bulkhead is floating and can be removed with no ill effect. You can cut the glass with a saber saw or rotozip. There will be a lot of fiberglass dust--this is toxic. You need to wear a good mask (best one of the carbon filter types)--and a Tyvek suit, as well as hood [also a stretch neck and head protection] and googles. put tape where you will cut to keep any splintering down.
I prefer to use epoxy to close any holes in the transom. You can add cabosil (fumed silica) to the epoxy to thicken. I would drill out the holes, and even add some glass fibers, if the holes are any size, or if there is any evidence of water in the core. I like to add a Starboard piece to put in other transducers on, without redrilling into the transom. Although some use Marine Tex--and it will work fine--I find that I like to make my own. Fiberglass workers don't like Marine Tex--because it has to be fully removed before any polyester lamination is done.
