Chris,
Most brazed up, lug built frames are assembled in a frame jig and the lugs are 'pegged' to keep everything lined up during the brazing operation. if you clean up the lugs, you will find small tell-tale circles of braze where the pegs are. When replacing tubes, I usually cut them flush with the lug, then find the peg (they are usually quite long and protrude well into the bore of the tube) and drill it out. Make up a boring bar that is a reasonable fit in the frame tube, then set a tool in it to bore out the remains of the tube. I don't like the idea of trying to melt the braze as it needs a higher temperature to re-melt the braze than it originally took to build the frame - and it is easy to damage the other brazed joints if the lug is overheated. You don't have to be particularly accurate with the size of the hole when boring out the tubes - the braze will disguise a multitude of sins!
With regard to your repair - if it is just the gearbox mounting tubes that have been cut out and need replacing, you should be able to remove the bottom half of the rear triangle by undoing the 2 bolts just above the rear wheel spindle. That will then give you access to the ends of the cut-off tubes. You will probably find that the lower frame tubes are one-piece (from the front down tube to the rear of the gearbox), in which case I would suggest that it would pay to remove the rear 4" of the engine rails, so that the replaced tube runs right through the lug. A sleeved and welded joint clear of any of the lugs will be better than a highly stressed joint in the vicinity of a lug. Like Mr Douglas, you should be able to fit new pegs to hold the frame in line whilst the joints are brazed.
Hope some of this helps,
Regards,
Eddie.