I'm trying to figure out at the moment what you're doing. It seems to me that you're using a more complicated method to get your problem solved.
First of all: did you reset your iPad after updating? (It's recommended, sometimes it will fix problems.) To reset your device (NOT connected to iTunes): press and hold Home and Power button at the same time until the Apple logo appears.
Next: you don't need to delete apps in iTunes (computer). If you want to reinstall them: open App Store - Purchased, tap the ones you want to install (with the cloud). Again: no need to connect your iPad to iTunes.