A method I've used to "catch" a threading tool once the setup and all else has been moved or disturbed is:
1. Clean the internal threads well, wash with solvent to remove oil. Paint the internal threads with Layout Dye (aka "Dykem Blue" or similar). When the layout dye is dry, follow Marka's instructions about centering the job when you set it back up in the lathe.
2. Set out quick change gear box to cut 5 threads/inch.
3. Setup your boring bar with the internal threading tool bit as you had it when you were threading the hub of the chuck plate previously. I leave the boring bar holder loose in the tool holder, and this is where my method my vary a bit from the accepted methods. Crank out the cross feed to there is no way the tool bit can touch the work.
4. Start the lathe in slowest spindle speed, engage the half nuts using the threading dial (aka "Thread chasing dial"). For odd threads, I believe the nameplate will state : "engage on any whole number". Engage the half nuts and let the carriage feed the boring bar so the tool bit is inside the female thread you want to "open up".
5. Stop the lathe without disengaging the half nuts. Carefully move the cross slide out until the boring bar/threading tool bit are sort of entering the threads. I zero the cross feed micrometer collar before running the tool bit clear of the work, and note how many turns it takes to clear the work. At this point, I move the boring bar so it is fairly close to entering the threads. If you move the compound rest, make sure it is in the direction of travel you will be using to feed in to cut the thread.
6. When you have the boring bar fairly well position, snug the toolpost lightly. Back the cross slide so the boring bar/toolbit clear the threads and disengage the half nuts. Run the carriage to a convenient location so you can use your center gauge (aka "fish") to make sure the tool bit is properly lined up for threading (I sometimes wind up putting a parallel or similar against the end of a job with a bored hole and hold the center gauge against it so I have something to check tool bit position against). Bump the boring bar as needed to bring the tool bit into correct position with the center gauge. Then, lock the tool post and tool holder solidly.
7. Start the lathe and engage the half nuts using the chasing dial. Let the carriage feed the boring bar/tool bit inside the work and then stop the lathe without disengaging the half nuts.
8. Bring the cross feed back to the zero you had it at in step 5. As you bring the tool bit into the threads, you may need to "tweak" the cross feed and compound rest's cranks a little to get the tool bit properly centered in the threads. If you have a small "dental" type mirror and a "penlight" or similar small flashlight, you may be able to get a look at how the tool bit is centered/entering the threads. When the toolbit is centered in the threads, roll the lathe over by hand- LeBlond having provided that handwheel on the 13" Roundhead lathes for jobs like this. You may want to shift the levers to a faster spindle speed so you can see things happening in a reasonable time. As you roll the spindle with the half nuts engaged and boring bar/toolbit seemingly centered in the threads, look with your light and mirror and see if any of the layout blue on the threads is being removed by the tool bit. Advance the compound until you start to see layout blue being removed from the flank of the thread on the side facing the direction in which the toolbit is feeding. At this point, zero your cross slide and compound.
9. Run the cross slide in so the tool bit clears the threads, disengage the half nuts and run the carriage out.
10. Set the lathe to a fairly slow spindle speed, as 5 tpi will have the carriage moving along quite rapidly. Run the cross slide back out to your zero point, start the lathe and engage the half nuts on the appropriate line. Let the carriage feed in and make a pass without changing anything on the cross slide and compound.
When you have made this pass, run the cross slide in so the tool bit will clear the threads, disengage the half nuts and run the carriage out.
11. Inspect the threads with your mirror and light to see if any of the Layout Blue was removed. Chances are you will see a faint bit of bright steel where the tool bit cut thru the layout blue on the flank of the thread in the direction the toolbit is feeding in. Back the compound out about 0.025"-0.050", then run it in to your zero plus 0.001". I call this "sneaking up on a cut". The reason I do this is there is "stick slip friction" in the sliding parts of machine tools. If you tried to crank in an additional 0.001" frm your zero point, you might not get it due to this stick slip friction. By having the backlash removed and the compound moving freely (having moved past the stick-slip friction to break things loose), I find I can get a cut of 0.001".
12. Take a threading cut with this 0.001" cut set on your compound. Check the bluing afterwards. If you have a male plug gauge (dummy spindle) made, try it. If not, you can take a chance and take a "spring cut"- letting the "spring" or deflection of the boring bar force the toolbit in for another very fine cut.
13. Take a "spring cut", a cut without changing any settings on your cross slide or compound. The "spring cut" will remove something less than 0.001". Inspect the blue on the threads and see how the toolbit is cutting. Chances are you will see the bluing is removed from one flank of the thread.
14. With the carriage run out, zero the compound rest micrometer collar and run the compound rest in about 0.025-0.050" to take out backlash. Crank the compound rest back out heading towards your zero, and stop an additional 0.001" beyond your zero. This will set the tool up to cut the other flank of the thread.
15. Follow the usual steps with the cross slide and half nuts to take another pass on the threads. This time, the tool should be skimming the flanks of the threads on the side "away" from the direction of feed.
This will ease off the threads with a cut on both flanks. I like to use the layout dye for work like this as it lets me see when the tool bit starts to contact the work and where it is "hitting" and cutting. It is very easy to overdo things when "easing off" a thread in the lathe. At the point you are at, even a spring cut can loosen the fit of threads a bit more than is needed. I tend to think that some spring of the boring bar is what bit you: namely, the boring bar deflected a bit more as the lathe advanced it into the work. Another thing that can bite you on this sort of job is the fact that the forces applied to the toolbit act on the boring bar, using it as a lever and can actually turn the toolpost very slightly if things are not really made up tight and clean. Burrs on surfaces of the compound rest and toolpost can result in less than good bearing contact between them, and under load, a tool post can turn. I stone these surfaces off from time to time, and wipe them well before making things up. A boring bar is an excellent lever, and the forces acting on it produce a "turning moment" about the center screw in your tool post or boring bar holder. Keeping things as close and rigid as possible is another key to this kind of work.
Before you make up your toolpost and boring bar for this go-round, take an oil stone and stone off the top surface of your lathe's compound (the top of the tee slot), and the bottom of your tool post or boring bar holder. When you do make things up, do not be bashful about pulling on the wrenches.
A lot of little factors can add up to bite a person when doing machine work. Getting a tool bit restarted to "pick up" an internal thread is a good skill to have in your hip pocket. Being able to pick up a thread and just skim off a thousandth or two is really a fine skill to have, and you have jumped into the deep end pool with this job, for sure. Take it slow, use the layout dye trick and pull the lathe over by hand to be sure the toolbit is where it needs to be before you take cuts under power. Slow and careful is the way, as it is all too easy to mess up hours of work and screw up expensive material.