First of all, welcome to the forums. The line you mentioned is a case vent hose and should run up to a hole on the inside of the upper frame rail. It does this to reduce the chance of sucking water into the case. The fitting on the carb is a vent also and should have its own hose. It also should run up to a second hole in the frame. You might have to remove the fuel tank to see the holes.
I know the "VOICES" aren't real but they have some great ideas.
1999 Sport 400 2x4
Complete rebuild w/Wiseco piston by Todd Kerby, Comet clutch, Swamplites front & rear, 03 Predator Rear Hubs,
ITP Pro Baja Wheels (4x156 front & rear), DG Front Bumper, Fuj Rear Grab Bars and RZR Belt