Pretty much as above, but close the halfnut and use the carriage handwheel to load the halfnut in the direction it will be loaded during the cut. Helps to have a flashlight to get it set. You need all the light you can get in the hole like that. I used to do a LOT of this when making and repairing hydraulic parts like pistons and tubes with damaged internal threads.
I would set up the lathe for internal threading, then move the cutter to a position just one or two threads past the start of the thread, lock and load the halfnut (by using the long travel handwheel to roll the carriage back towards the tailstock and take all slack out of the leadscrew), then juggle compound and crossfeed until I got it all centered up, then zero compound and crossfeed dials. Back out a ways, fire up and close the locknut to chase, but with the crossfeed a turn in to prevent engagement of the cutter. Let it run in a few threads, then stop the spindle and crank the crossfeed out until it zeros and touches. If it all works out right, you are set to chase ...if not, start over with locking and loading the half nut and juggling compound and crossfeed until it works right.
Reason for repetition is that you can get slack in the half nut and leadscrew, but also in the gear train between the spindle and QC box, as well as in the QC box itself that can change the position of the cutter once you start trying to actually run the lathe to cut the thread. Your fit problem could have been caused by no keeping the machine loaded when threading, too. Again, when cutting a thread with any lathe, I drag my hand on the carriage handwheel to keep everything tight. If it wanders on the first cut or two, the tool will tend to follow the imperfect thread if left to float. Same for light last passes, in that it may cut more on one side or the other. Keeping that steady load on the handwheel prevents the cutter wandering.