Standard way to deal with this sort of dilemma is to leave the half nuts engaged and work with the topside set the parallel to the bed. Exact replacement position becomes a non issue as the topside provides the necessary fine adjustment to give proper alignment between thread and tool.
As Neil says its important to use the threading feed to run up to the approximate position to take out backlash.
For final adjustment I prefer to cut on the front edge of the tool as its easier to set up a very fine skim.
Can be a pain in the backside keeping track of cuts. Best way is to start by touching the tool off the workpiece.
Set the cross-slide dials to zero.
Crank the saddle clear of the workpiece and run the cross-slide in by the book thread depth (plus an allowance for tool tip shape if yours is too pointy).
Set the cross-slide dial back to zero.
Cut thread as per normal using only cross-slide feeds. When the dial gets to zero thread should be the calculated book depth.
Remove, test fit and adjust as needed.
I normally use the zero2zero threading method where the lathe self generates the required in-feed with the topside set at close to half the thread angle so this is a simple modification to my standard process.
Got me a left hand 26 TIP thread wheel bearing retaining ring in the "Please fix this for me" box that will need this approach. On machine trial fits are a bit impractical with a 19" diameter motorcycle wheel. With a simple job like that its easiest to make a test piece then revert to the zero2zero method for proper job as the final cross slide dial reading give the extra in-feed needed beyond the original setting so the proper depth can be used.
Clive.