Such is the joy of not using kits, there are no rules.
The basic idea is that you want enough thread that the parts are held secure and the force is distributed across enough material that a little extra torque when closing won't take the threads off the parts. You also don't want so much thread that an inordinate number of turns are required to separate the parts. Sections don't come off often, so you have some liberty there, but caps should ideally come off in less than two turns.
My cap threads are almost always 30TPI triple start which means the lead is .1". This is very close to the typical m13x.8 tripe start taps and dies that are popular which are just a tiny bit finer/slower. (2.4mm vs 2.54mm for the .1".) For each turn of the cap, the cap moves .1" So to keep the number of turns under two, the thread engagement needs to be under .2". A tenon should have a reduced or chamfered end where it meets the section. My preference is to have both. I'll cut the tenon end somewhere between .025" to .1" at the same diameter as the end of the section which must be smaller than the minor diameter of the thread. I'll then have a 45 degree step up to the major diameter of my thread. The length of the tenon then needs to be long enough to accommodate the .2" of complete thread plus whatever over run. It'll also need to have some clearance length for the die or threading tool if the barrel is larger than the tenon, which in my case, it usually is, but not by much. I don't like large steps, but I like a clean delineation between the threaded tenon and the barrel. It's purely cosmetic. (As an aside, large steps and flush cap to barrel joints are popular, but they're kind of awful from a user standpoint. Some people don't mind them, but a great many people do. Also, there's no reason to cut a relief behind the threads on the tenon. It makes the joint weak and frankly, it looks terrible.) So now we have a tenon that's long enough to get two complete turns of a cap.
Onto the cap. The inside of the cap should have three different bore diameters. The deepest and smallest should accommodate the nib. The next should accommodate the section and is usually the minor diameter of the threads although it doesn't have to be, that's the simplest. The last is the relief to pass over the threads and any unthreaded portion of the barrel tenon. Here's some things I see that are often missed. The section should stop on the shoulder between the nib part bore and the section part bore. That accomplishes several things. It provides a hard stop. Stopping on a square shoulder is more positive and much safer than stopping my running up to the end of the thread. Stopping on the cap lip against the step at the end of the tenon can cause the lip to crack. It seals the nib from the outside air preventing it from drying out. (My pens can sit for months without drying out without resorting to o-rings or other gimmicks.) This method also works equally well whether or not the tenon and barrel are the same diameter or if they have a step, but the when there is a step, it must be measured and cut carefully so as to prevent the cap from stopping on the lip. The last relief cut needs to be deep enough to clear all the unthreaded and partially threaded portion of the barrel tenon. I usually cut mine just a couple thou, at most, larger than the tenon. If you then want to reduce the number of turns required to cap and uncap the pen, this relief can but cut deeper. Cutting the relief deeper should have no other effect as the cap should still be stopping when the internal shoulder hits the front of the section.
Those are my thoughts on the matter. Hope it helps.
