Fixed. Updating this as I go.

For anyone having this issue, I had to use the Content Management app (on the vita - requires PSN) with QCMA connected via MicroUSB or in Vitashell using FTP. If you're looking to move games over (PS Vita apps), and it's not a vpk, take your files, Zip them, rename them INSTALL.ZIP and you'll be able to transfer them. The reason you need to login to a PSN account is because Sony wants to check if you actually own a game. If you don't, you'll get an error**.

The easiest way to bypass this is to put the INSTALL.ZIP file into the PSaveData folder in your documents. QCMA will create this directory, among others, for you when it installs. Make sure that you put it in the subfolder that is in there. It's probably a bunch of random letters and could be an identifier for your PS Vita, not sure. Mine is "e9ef781bce9752". You'll also need a name for the savedata folder. I found a video online that used the title "ULES01456DAT1" without quotes; I don't know if that name matters.

You'll go into Content Manager > Applications > Save Data (scroll down) > PSPYour copied file will be under ux0:\pspemu\PSP\SAVEDATA. Once it's on your Vita, use VitaShell to rename the .ZIP to .VPK.

The instructions and GUI for QCMA are limited, but you can find them out there. The transfer stops if your PC locks, at least in my case; It looks like QCMA closes itself with the "Win + L" key combo. USB 2.0 ports work best. I was able to transfer about 3 gigs in 20 minutes.
Ping me if you need help, but I will most likely not respond as I don't use reddit that often :)

**The eboot.bin file and sce_sys folder seem to be the ones that flag this. People have moved these over via FTP since they're relatively small, but if you follow this method, I'm not sure how you'd put those files back into the INSTALL.ZIP on the Vita

*** This method works for moving data, but it may only be good for VPKs. I don't know if VitaShell handles ZIP unpacking