Hey Justaerin,
I had the same problem with my 04 'Bolt, definitely check your primary chain tension, but also make sure your clutch and clutch cable are properly adjusted.
Your primary chain (at least mine) is supposed to have 1/2" to 3/4" play. Mine has 3/4" and is quiet.
Next adjust yoour clutch by:
1- shorten the clutch cable housing, get lots of slack, say a 3/8" gap at the clutch lever perch where the cable enters the clutch lever perch. Loosen the lock nut and screw the adjuster nut to make the cable housing shorter, increasing the gap at the clutch perch. You want to make sure that the cable is not pulling on the clutch ramp at all when you screw the clutch ramp adjuster screw all the way counterclockwise till it bottoms.
2- Remove the clutch inspection cover and remove the spring and lockplate. Using a flat blade screwdriver turn the adjusting screw counterclockwise until it bottoms gently. Check that there is no tension on the clutch cable. Now turn the screw 1/4 - 1/2 turn clockwise. Replace the spring and locking plate. If the hex on lock-plate does not align with the recess in the outer ramp, rotate adjusting screw clockwise until it aligns, but don't go beyond the 1/2 turn. If you have to rotate it the adjusting screw in the other direction till the lock plate fits, but make sure you still have the minimum 1/4" clockwise turn.
3- Adjust your clutch cable so that when you pull on the clutch cable housing away from the clutch lever you have a 1/16" - 1/8" gap between the ferrule (metal end of the housing) and the clutch lever bracket
Once you get all those adjustments done that is about as good as it is going to get. As Steven says, you should also be running 20-50W full synthetic in the tranny.
I did all those adjustments and I still got a pretty good clunk and sometimes the bike would even jerk a bit when I shifted from neutral into 1st.
I just recently installed a hydraulic clutch from ASB and after adjusting the clutch per their specs for the hydraulic clutch my bike shifts into first smooth as silk, no more clunk/crunch or jerking of the bike, it is wonderful. It also seems to shift better through the other gears as well now. Plus now the clutch is an easy 2 finger pull. Not a cheap mod, but well worth it.
Good luck