Rewiring, changing ape hanger handle bars to std

The only thing I could think of without hacking the seating area up is to, put some taller risers on your handle bars to raise them or buy a set of mini ape hangers. Mind you, if you go too Tall with the bars or real tall risers you may need to buy all new (Longer) cables for your controls. If it were me, I'd buy a bigger bike to fit my size and frame.

Have you considered the kill switch or ignition might be different.

Either measure it with a tape measure or measure the standard bars then the height difference with you apes and add that to the standard cable length

go to the harley dealer near you and explain your problem, I don't know if they still have them, but you could used to get the top clamp for after market bars that had a smaller diameter, they weren't that much and bolted right on,

On the handlebar switches, Harley hasn't changed the color code scheme very much over the years but you really need a good schematic to know exactly how they are wired up. If you can find either a Harley service manual for a 96 model or a Clymer's manual, it would be helpful. I have a schmatic for a 94 FXDWG that should be alright for your 93 FXR but you need a schmatic for a 96 model bike.