My suspicion would be the tranny also. If it was a clutch problem you would have been able to get it out and into any gear. A locked up back tire will be the result of two things…a seized brake or transmission issue. The clutch’s only purpose is to disengage the motors spinning from the transmission to allow you to hit the next gear. For instance found this for ya:
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Motorcycle Transmission Basics 101
The typical modern motorcycle gearbox or transmission is a “constant mesh” design. The name comes from the fact that all of the gears in the transmission are in constant engagement with one another. This differs from some older designs where the gears slide back and forth on shafts, engaging one another one pair at a time. The gears are arranged so that you have a drive gear, coupled to the engine, and a driven gear coupled to the rear wheel. They are arranged on shafts, the drive gear on the mainshaft and the driven gear on the countershaft. In most cases, the mainshaft is driven directly by the clutch, which in turn has one set of plates connected to the engine and the other set connected to the mainshaft. Most clutches are driven off the engine’s crankshaft by a gearset as well. They may use direct gears or a chain or belt drive. This is called the primary drive.
The countershaft drives the transmission’s output device, typically a U-joint in the case of shaft drive, or a countershaft sprocket if it’s chain or belt drive. This is called the secondary drive.
One of the gears in a pair of gearsets, will be coupled to its shaft, main or counter, at all times. The other gear in the pair will rotate or spin freely on its shaft on bearings. In between the free rotating gears and splined to the main or counter shaft, are the engagement dogs, or at least half of them. The other half is built into the face of the gears themselves. Each free-spinning gear is then coupled to its shaft by the engagement dog. The engagement dogs are typically one of a few designs, but all of them work basically the same way. The first use multiple fingers and corresponding holes, typically in the gear itself. Others have fingers built into the gear and the corresponding holes in the engagement dog. The Valkyrie’s transmission is built this way. Another type is a blade and slot design. There will be a pair of blades, looking much like common screwdriver tips, on the engagement dog and a set of corresponding slots in the gear. Usually there will be twice as many holes or slots as there are fingers or blades. This is done to aid engagement speed as the dogs and gearsets only have to turn half as far to engage. Older Gold Wing transmissions use the blade and slot arrangement for example. They can be slower shifting than the finger type engagement dogs, but provide a bit more torque handling capability for a given size dog and gearset.
To move the engagement dogs back and forth along the countershaft, they have a slot cut perpendicular to the shaft into which a shift fork fits. In turn, the shift forks are moved by the shift drum that is rotated by a selector mechanism, typically a ramp and pawl design. The shift drum is designed to select only one gear pair and engagement dog at a time. Because of the different ratios, if two or more gear pairs are selected at the same time, the transmission will be locked and unable to turn.
Now here’s a hint for you troubleshooter types: If your engine runs OK but stalls out when you start to engage the clutch, and the bike won’t roll freely, you’ve just found your problem. Your transmission is locked and probably engaging more than one gear pair at a time.
reference: http://www.wootbike.com/articles.php?article_id=3&page=1