Once the panels are out you need to get rid of the beading on one side to get glass in. Ideal job for a router really but, to saw it off, I'd try a tenon saw against a batten, at least on the long lengths. The short sides will probably be too short to get any movement on the saw. You might even get away with a Stanley knife on these. It doesn't have to be that neat a job as you can always tidy up with a chisel. Or use a wide chisel for the whole thing if you feel competent. Try and keep the line straight though. Chances are the glass will be thinner than the panel, so this cut will be an exposed corner when the new beads are in. I'd use a general purpose sealant to bed the glass in. You don't want anything that's going to dry out and rattle. Take the door round the glaziers if you're fed up with it all by then. I know I would. Probably quicker to do all this than explain it