6 speed rebuilt transmission - anything to look out for?

so i have a 2012 tsx se 6 speed that had an aftermarket stiff clutch and a short throw shifter. i bought the car from some random guy whom said he didn't know any history on the car (red flag, but i thought i was getting a good deal). anyway, 500 miles later while cruising down the freeway at 70mph, it felt like the car downshifted into 2nd gear or something and the engine hard braked for me so i pulled over right away and shut off the car. after a couple of minutes to make sure i didn't overheat or have an engine leak somewhere, i restarted the car and it was creeping forward regardless of where the shifter was, even in neutral! however, it didn't go over 5 mph and it felt like the gears were grinding while it was moving. seemed like it was stuck in a gear despite the shifter location.

i ended up towing the car to the nearest honda dealership (the car was obviously resisting being pulled onto the tow truck and was jerking... prob made it worse!). the dealership said i needed a new tranny. so they ended up finding me a rebuilt tranny, which will come with new oem clutch of course, and oem axles. 4 weeks later, it's now ready to get picked up.

has anyone ever had to rebuild their tranny before, or get a rebuilt one installed? do i need to break-in the tranny or anything specific? and has any problems arose anytime afterward?? just trying to plan ahead when i pick up the car this week.