I reckon theres been a problem with the whole primary. It ran with almost no oil for 50 miles? Thats going to root the chain. Did anyone previously remove and refit the the whole primary side, i.e. clutch out, alternator off etc? If so, if the inner case has not be shimmed square that needs to be looked at. Distrorted cases will lose oil. The primary chain has to run in alignment with the engine drive sprocket, otherwise the problem is going to repeat itself, chain stress and excessive wear.
I seriously recommend you pull the whole primary, clean eveything, examine the clutch basket and plate splines. If they wear and dig in they create difficult shiting and may grab or slip. NOTE - some aftermarket plates have wrong spline profiles! Get genuine or guaranteed quality plates. A Commando clutch should be smooth, dependable and allow a seamless gear shift. Fit the inner case with a new crankcase gasket and the relevant shims on the centre bolt to align with the case joint on the crankcase. Fit a new primary chain and re-align and re-tension the gearbox. Grease the rubber band seal before fitting up the outer case.
Inside the gearbox outercover is the shift quardrant movement is controlled by a forked spring. That spring sets the quality of the shift with positive engagement. WIth the shift lever attached, move the lever down 2,3,4th and up 4,3,2,N,1 and obsever the arc of the quadrant enagement. The spring forks just contact the shifter equally on both sides. Too much on one side biases the shifter and changing up or down is going to be compromised. My way of adjusting the shift is to tweak the spring fork at the point of contact on the shifter with pointy nose pliers. Carefully bend it so it just touches the shifter and both forks are equal. Check the arc movement of engagment. If all seems good, just refit the outer cover dry and rotate the back wheel whilst shfiting through the gears by hand. If you get positive selection of all gears up and down, remove the cover, fit gasket and bolt up the case. Use a good quality 80-90W gear oil.
The above was recently carried out on a '72 Combat and resolved slipping and shifting problems, hope it helps.
Mick