Unless you have a shop full of tools, you may not save much. Poor material and joinery will quickly tell on windows. Removable panels adds another degree of difficulty. The typical dimension for storm window stock is 1 1/8" thick and 2 1/4" wide for top rail, mid rail and side stiles, and the bottom rail is 3 1/4" wide. You could cut the rabbet for the panels first, and complicate the joinery, but IMO end up with a better job, or build the frames plain and rout in a 3/4"w. x 3/8"d. rabbet afterward. You can also run a 1/4" corner bead molding around the outside of the openings to lessen the water-trapping ledge, as the rabbet faces inside.
Once you build the frames you will be able to measure for the screens and plexiglass (or real glass). They will make the screens with aluminum channel about 5/16" thick and 7/8" wide, and this will sit inside the rabbet and be retaned with small turn button clips made for this purpose.

For joining the pieces, some people seem to have luck just using biscuits and glue, others prefer screws into end grain, but I really only trust through mortise and tenon joinery.
Casey

I usually avoid through tenons to reduce the end grain exposure.