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You don't have to remove the primary to remove the shaft...there's a bolt that holds the shifting rod on just like the shift levers. Loosen all three and you can pull out the shifter shaft.
The OP talked about the toe and heel levers being loose so that pretty well means the front shaft. The shaft can be easily removed from the primary case by removing the inner shift arm, then the shaft just slides out. If the OP is correct that the splines on the shaft are damaged, he would be wise to also replace the heel and toe levers. If all of those levers are kept tight, they will last the life of the bike. If they get loose, the splines will round off or strip completely. He should absolutely check the tightness of the lever on the transmission to make sure it is solidly tight.