3/32 diameter rod can be threaded with a 3-48 die without issue. A 3-48 thread has a basic diameter of .099” which is only .005” larger than the 3/32 diameter rod (.094”). Since commercial screw threads are typically .001” -.005” smaller than basic diameter the 3/32 diameter rod is almost perfect for a 3-48 die. I have not found any scale size nuts larger than 2-56 but if the nut size doesn’t matter a 3-48 die on 3/32 rod will work fine (you can also make your own scale nuts). Additionally a 2.5mm die (.45mm lead) is essentially the same size thread. As long as you use some type of lubricant on the brass and a thread, unthread, thread again motion you should never break a hardened steel die on brass rod.
As far as standard rod sizes, a 5/32 rod can be threaded with a 4mm die (.7mm lead).
To determine the basic diameter of a numbered screw multiply the numbered screw size times .013”, and then add .060”. For example a #3 screw will be ((3 * .013”) + .060”) or .099”.