Apps missing after restore of iPod Touch 4th gen.

I think I may be beat. I had to do a reset erasing all content and settings to cure a problem where all data on my iPod had starting show up as the actual data AND unknown, essentially doubling the footprint and almost filling it up. It's happened before and a reset\restore fixed it.

This time, I restored it, and most of my apps didn't come back. I went to apps and tried to set them to "will install", and they don't install. I tried installing one from the store (Mercury browser) and it tells me that I can't unless I have IOS 7.0 or higher (which doesn't exist for my iPod).

I tried restoring both of my backups with the same result. I have the latest IOS for the device @ 6.1.6.

What can I do to get this thing like it was prior to my reset? I figured a restore would do it (I back it up daily), but I guess I figured wrong. It seems like it's not really backing up what's on the ipod, but noting the apps, then installing the latest (not what was actually on there). For me, that's totally screwing me up.

I'm hoping there's a process that'll save the day for me.

Thanks.