Yes, the leaking head is likely the result of the high temperatures. The head and cylinder should be checked for warpage.
The base gasket seals a coolant passage as well, from the cases up through the cylinder.
Did the bike have a plastic impeller? If so, also the possibility that you lost that and things cascaded downhill from there.
Just an FYI, on the bearings, the '07 uses a two piece roller on the ignition side. This bearing runs a high clearance compared to the ball bearings you are used to on the older motors. You can detect what appears to be excessive radial play but it is normal.
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