I have never ran one without an air box but, I would start richer than stock.
http://www.vintagevmax.com/1986_service.htm
Carburetor- Mfr.- Type/ Size/ Qty/ ID Number Mikuni- VM38/ 38mm/ 2/ L:80N-00 R:80N-00
Main Jet/ Main Air Jet 290/ 2.5
Slow Jet/ Slow Air Jet/ Air Screw �/ �/ �
Pilot Jet/ Pilot Screw (Turns Out) 40/ �
Needle Jet/ Jet Needle- Clip Position/ Cut Away/ Air Jet Q-0/ 6DH1-4/ 3.0/ �
Power Jet/ Power Air Jet L:135 R:130/ L:1.5 R:1.4
Fuel Inlet Valve/ Float Level 1.5/ 18.1mm
Idle Speed 1500 rpm
VMX 540 K High Altitude Specifications
Standard Settings High Altitude
Idle 1500 rpm Standard
Clutch Engagement 4000 +/-200 rpm 4200 +/-200 rpm
Shift Speed 8200 +/-200 rpm Standard
Main Jet # 290 See Setting Chart
Slow / Pilot Jet # 40 Above 6000 ft: # 45
Pilot Screw 1/2 Turn Out Above 6000 ft: 1.0 turn
Jet Needle Clip Position # 3 # 3 or As Needed for Response