I am not entirely sure what is wrong after doing this upgrade.

I was on version 2.4, so I had to do a double upgrade. First I upgraded to version 2.5, and everything seemed mostly normal (other than some template tweaks being gone). Then I upgraded to version 2.6, and suddenly I have no featured videos being displayed (even though they are selected in admin) and my tags box is totally empty. Plus there was a "video of the day" I had added to my index.tpl and that is still showing, and I dont see how since the index.tpl was overwritten.

I'm totally confused.