I'll play, but please realize that there are no rules, these numbers should be what you (and eventually your customer) find appealing.
For now, I have focussed on building around JoWo #6 nibs, the section-to-body junction threads I am using are M10x1. The cap-to-body threads are M13x0.8T. Length wise they are sized to be used with a standard ink converter (with is a few mm longer than an international ink cartridge when in place).
For the 10 pen series in progress (all wood with inner liners), the length of the capped pen range is 137-142mm, with the cap length of 65mm +/- 1mm, and the body length (excluding the threads) range of 76mm +/- 1mm. The cap diameter range is 14.9-15.3mm, and the body diameter range is 14.4-15.0mm (at the widest, at the cap-body junction for both). The body inside is drilled with a 9mm bit, the widest drill bit for the cap is 31/64". Sections are in progress, the length is typically 25mm (excluding the threads for body junction), and the smallest diameter is typically around 11.2mm with the widest drill used for hollowing at 8.5mm.