I think you can contact Ultrasabers CS and ask for the ordering procedure for a Micro USB. They will probably ask you to choose the Mini USB and put a not in the Order Comments (during checkout) that you want a Micro USB instead.
It's possible that you have different board generations in your sabers. The older boards such as the initial Emerald and Obsidian v3 used a Mini USB, but the newer ones (especially Diamond) use a Micro USB.
As for the Recharge ports, Edon already covered everything
Just do the same - contact CS, ask for the procedure and then follow their instructions during the order process.