Sounds like a simple case of a dead battery? Buy a new one! What could be easier?
I have never liked Power commanders on Vstroms. I'd toss it. It just sucks fuel. Total waste of money.
Disconnect your NEW battery and F.I. system should re-set to de-fault ECM mapping and will get better as it adjusts to your current altitude.
Running with a very low or near dead battery is a really good way to RUIN your Stator (a $450 part!) or RUIN your Rectifier/Regulator.
How old is your current battery? When it did not charge back up, this is a good indication it is finished ... for good. The P.C. just makes things worse, hurts fuel economy and confuses the ECM.
Hopefully you have not damaged any major systems. F.I. bikes must have a good battery. This is page one.
Any Suzuki dealer ... even if they do not sell the Vstrom .... should be able to order parts for your bike through Suzuki. If they have a computer and can get onto Suzuki's site for ordering parts, then they should be able to do it for you. Even Outboard motor places!