2nd gear grind
 

When shifting into 2nd gear, it grinds. I would have to shift very slow for it not to. Also, I feel like 3rd gear is starting to grind. Around how much will it cost to fix this? Its an MKIV non turbo.

Sounds like your syncros are going. Rebuild will probably be ~$1500. You can look for used tranny but there are no guarantees on what condition it will be in.