In addition to the occasional muster roll or pay roll from the black hole period, there are the hundreds of postwar pension applications which claim service during that time, not to mention postwar written narratives and family oral traditions. So it's safe to say that men didn't quit joining up after March 1864, it's just a lot harder to find the documentation.
You're right that the Gerdes site is getting more and more out of date. I've toyed with the idea of starting up a new website, but that would involve a major investment of time and energy. Currently, I'm using the Arkansas discussion board to post updates until I can figure something else out. The advantage in using this discussion board for updates is that I'm a beneficiary too. Just yesterday a gentleman posted some information regarding a Virginia pension application from a veteran of the 18th Arkansas Infantry. I've been adding helpful little tid-bits like that to my database for years, and over time it really enhances the information I have on each soldier. Unfortunately, those 85,000 names include a lot of "mystery men" whose identity cannot be positively determined -- a whole bunch of J. Smith's, for example.
To add to my fun (or misery) I am also working on a similar database for Louisiana soldiers. It's not nearly so far along as the Arkansas database, though. I had always planned to set up one for Missouri soldiers, but I'm probably too old to even think about that now. We'll see.