There is a proper way to do plug reading to know how your bike is running. Riding around at various speeds and returning back to the shop to pull the plugs to read the color is not getting the accurate reading.
All tuneup procedures must be done before you take it out on a test run. New plugs for each change to get accurate readings.
A description on getting a good reading.....
What is a plug chop?
A plug chop is referred to taking a motorcycle out on the road at certain speed and RPM for a few minutes, without changing the throttle position. Once the few minutes are up, the rider quickly pulls in the clutch, shuts the engine off, and coasts to a stop. Once pulled over, all plugs are removed and the spark plug color is inspected.
What should I do before a plug chop?
Simply put, the motorcycle should be in great running condition.
The electrical system should be putting out over 13V to the battery.
Valve lash must be within specification for even compression.
Proper point gap and ignition timing if applicable.
No vacuum leaks.
Carburetors must be synchronized.
Install brand new spark plugs.
I've not dealt with makuni carb conversions, though have seen them, so I can't comment on them. You said 1&4 are manifolded together and 2&3 together??? Do you have special intake manifolds??? The usual set up is 1&2 and 3&4 together.