I've had some the same problems with NARA too. My great-grandfather, an ex slave was a body servant for a confederate general and I haven't found any information for a civil war pension, but from some letters my g-grandfather wrote in the 1920's states he finally received a $50.00 per month Indian war pension(Buffalo Soldier, 1867-72), I believe in 1929. I jumped thru all the hoops from NARA, several forms and letters to several cities. Finally they told me the VA Adm. had the file. So I started over again, at my area VA, then DC and at some point I received a Pension # which I've used...so I'm still waiting, one year and counting.(one letter did tell me I could come to DC and look or hire someone to find the record) Best of luck with your search.