I would also try uninstalling Bootstrapper first & take the over the air again.
Some of these apps create issues with the update process.
You wont lose any apps, settings or data if you update OTA.
I would also recommend moving all of your photos & Music off the sd card onto the computer temporarily while doing the update & than putting them back after the update.
It is a known issue that a lot of media files can make the update take a really long time. (several hours)