There are internal pull-ups. And EasyHID configures them for Full-Speed, so you shouldn't need external ones.

Did you use all the configs from post #11?

In particular _VREGEN_ON_2L.

Your original configs had that turned OFF, just want to make sure it's turned ON now.

Should I take out that define statement?
It doesn't really matter, it's fine even if not using a bootloader. But if you were using a bootloader it may have caused problems with the config settings, so I thought I'd ask.