Welcome to RME!
What's your primary use for the Jeep? If you spend much time offroad, an automatic trans is way easier to drive offroad than a manual. You could swap in a 700R4, get a deeper first gear ratio and gain overdrive, both would be a great match to the 350 and the Jeep.
If you wanted to swap to a 5 speed, it would take a decent bit of effort... adding a clutch pedal, hydraulic master and slave cylinder, etc.
Either way, you will probably have to move the Dana 300 back a little and shorten/lengthen driveshafts.
If it were me, I'd buy a quality rebuilt 700R4 and go that route.