Mike,
These symptoms are spot-on for a corrupt install… could you try (for sanity sake) to download our 5.1.1 All in One installer (190mb) and run it. Install it to a brand new location, make sure you don’t install it to an existing location and then run it, and open your workspace and see if it behaves itself?
Missing perspectives, app server connectors, etc. seem to be the first plugins to die (fail initialization during startup) in a bad install… so I’m hoping the new install fixes that.