Partisans were allowed full cost of any captured weapons turned into the Confederate Ordnance Dept. Much like privateers and captured booty. (Confederate Public Law). That could mean lots of money to be made.
But even if the trooper were not making any extra money turning in captured weapons there were other and legal ways to increase his pay. Just like todays military soldiers and troopers were paid a base pay so the the Confederate soldier. In 1864 the pay for a trooper (private) was $12.00 a month. If he carried his own weapons, he would be paid $1.00 a month for each weapon. Lets say, two pistols, thats now $14.00. If his command is on detached duty, away from their base of supply and rations, like many cavalry units were, the commuted rations pay could be as high as $.75 a day (1864 Confederate Army Regs). The amount of commuted rations pay was according to if the time spent was in a urban area or in the country. So it was possible for a trooper private to collect, when he got to the pay table, $36.50 at the end of the month. Let's say he didn't get paid for six months, not unheard of. He could collect $219.00 lump sum, maybe more if their were more pay and allowances that I did not cover, like uniform allowances. Almost every personal cost to the trooper, if it was allowed, could be reembursed with pay allowances. So if the trooper were assigned to a post were all the needed required needs were provided to the trooper he may see just $12.00 when he came up to the pay table. Many had to be supplemented with extra allowances, just like today.
As for every unit in Virginia (and S. Carolina) submitting to a I.G. inspection every month, no wonder Lee lost! Thats unheard of today. In my experience with I.G. inspections, ours were scheduled, and we had several weeks of preperations. The inspections lasted on average two weeks. Failing an I.G. could and would lose a commanding officers job. When did these units have time to fight?