Did you know that Cisco Autonomous access points can be upgraded directly to LWAPP access points without using the Upgrade Tool? It's true. Use this command:
archive download-sw /leave-old-sw /force tftp://ip-address/image
Then verify the system boot image was set correctly, which should happen automatically with the command above:
Then simply reboot the access point. The controller discovery mechanisms also need to be in place for the AP to find a controller over a layer 3 boundary.
The only real reason to use the Upgrade Tool is if you have a really old access point that was manufactured without a MIC (manufacturer installed certificate). In that case, the Upgrade Tool issues commands during the upgrade process to generate a Self-Signed Certificate (SSC) on the AP.