The long version of +1 on tight primary chain
Chain adjustment is an art form. It only takes one tight spot in the run of the primary chain to make it too tight for the gearbox. Chain has to be checked all the way around more than once during assembly. Fortunately it's easy to adjust after the fact without removing the primary cover. Move the gearbox forward incrementally in small steps and test until shifting feels right. You have to adjust/check both the primary and rear chain at the same time more or less. Rear chain should be adjusted with rider weight on the seat feet on the pegs, but you can fake it till you make it. A little loose is always better than too tight.
If you worked on the gearbox while the engine was apart, that could be part of it. Could also be the clutch not disengaging from the gearbox easily. Clutch center notched too much, excessive gear oil leaking onto the friction plates, over torque on the big nut holding the clutch on the gearbox main shaft. I'm not that familiar with Commando clutches. Many after market manuals sight around 20 ft lbs too much torque, or so I've been told.