Alright so I recently changed out my primary cover on my 98 sportster and now I can't get the clutch to work at all.

 

Look for that spring that fell in the floor when you removed the primary and or derby cover. It's a small spring that inserts over the jam nut where the adjuster screw is. If thats not it, be sure one or more of the 3 steel ***** for the ramp assembly where the clutch cable connects became dislodged from the groove they ride in. After checking that, remember the adjuster screw turns counter clockwise to adjust the clutch. Screw it out until (ccw) until resistance is felt then back off 1/4 turn. One of these three will fix your problem. Stroker

 

Well ... the cover does not come in contact with the clutch hub so there's no reason for it to impact your clutch.

Did you release the cable or make any clutch adjustment during this repair?

I'd say it's a separate issue altogether.