I plan to do the same with my t2000 to FRP box, however all the cuts I have made through my frp which includes window openings, doors, slideouts, vents etc.... I have done 2 coats of urethane on all the freshly cut wood. If water gets in there it will delaminate and will be ruined. I have cut my pass through yet and am not sure how that looks but I would think some kind of silicone around the edge wouldn't hurt.
As far as cutting the FRP, I just use a carbide tipped blade on my circular saw and either a jig saw or saw sawzall for the corners. The FRP is pretty hard on blades. As far as the back of your truck wall, I would use the same circular saw blade as it is thin sheet metal and will cut it pretty well. The blade will be junk when you are done but it will be straighter than trying to cut it out with a sawzall.
Steve
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