Some info is out of date, or operators no longer in business.
To my knowledge, of the east side shuttle services listed, only two are really in business, are insured and licensed and have a track record
Bob Ennis in Lone Pine and High Sierra Shuttle in Bishop
http://www.mtwhitneyshuttle.com/http://www.highsierrashuttle.com/as for where to go for a partial JMT - I'd always do the southern half - much more spectacular.
Join the yahoo group for the Muir Trail and you'll get more info than you may be ready for - there are a few hundred JMT hikers with cabin fever waiting for anyone to ask questions. Today they are off on a long ultralight gear tirade thread again
http://groups.yahoo.com/group/johnmuirtrail/