The parts you should replace are correct, rear main seal is cheap($6-$8) but hard to get to unless transmission is out.
For clutch parts you need self-adjusting pressure plate, clutch disc, slave/throwout bearing and pilot bearing, master cylinder is optional but not a bad idea, but you can always change it later.
Ranger clutch system is a real bear to bleed.
What you describe is what happens when the slave cylinder doesn't push out far enough and the clutch disc is still touching the flywheel.
This means the Input shaft of the transmission is still turning with some torque, pushing on the stick shift puts pressure on the synchro bushing/gear so it tries to slow down(or speed up) the Input shaft to match the Output shaft speed.
If Output shaft speed is 0, truck is stopped, then Input shaft has to stop, if clutch disc is touching flywheel, even a little, it gets very hard to slow it down.
This is generally caused by air in the system but it doesn't go away.
Why it would come and go is a mystery?
Doesn't read like a transmission issue but since you don't have a history on the truck changing the trans fluid might not be a bad idea, pay attention to what drains out.