Firstly I don't know the Yam's but are you sure you cannot unhook the return fork spring on the shift selector shaft and then turn it aound so it wil clear the clutch basket?, try this first.
If you find you definitely need to take the clutch basket out then you will need to do the following:
Remove the five(six? Yam?) clutch pressure plate bolts. These are usually not too tight, and can be undone with a quick spin with the correct sized socket.
Remove all the pressure plates, friction plates and driven plates(the steel smooth ones) in a chunk. Keep all these bits together they need to go back on in the same order.
Now in the middle of the clutch basket is a large nut, aboout 22m, which probably also has a locking washer thay may be crimped over to hold the nut. Flatten this crimping with a punch if needed, and then undo the nut.
NOTE...this nut will be extremely tight, DO NOT USE THE CLUTCH BASKET TANGS, OR THE INNER HUB TANGS TO STOP IT ROTATING- IT WILL BREAK AND COST YOU LOTS.
You will need to make or hire a 'clutch holding tool', spk to your local garage to see if you can borrow one.
Once you get this nut off, then slide off the inner hub and clutch basket (again keep all bits in order for later rebuilding)
Now you should be able to get the gear shift shaft out.
If it has been welded in the past, the oil seal on the LH side is probably knackered, so get a new one, also would be a good idea to replace the washer that was crimped over. YOu will need to do all the bolts nuts up back to the proper torque setting as per the manual.
Hope this helps, Sully