If you transferred all of the purchases into iTunes, the apps should have synced back at the end of the updating process. So try this.
Connect the iPad to your PC with the cable and launch iTunes if it does not start on its own. Enable the sidebar again if you need to do so. Click on the iPad name under the devices heading, then click on the Apps Tab at the top of the iTunes window on the right. You will see a list of all of your apps. Click on the Sync Apps heading to make sure that it is selected - put a checkmark in the box next to the heading. Then go down through the list of Apps and click on Install for any apps that are not already on the iPad. Then click on Apply in the lower right corner of iTunes.
You can also download your apps again in the Purchased tap of the App Store directly on your iPad. Go to the App Store, tap on the purchased tab and then tap on Not on this iPad. You will see all of the apps that did not reinstall. Download ONE app at a time until you have recovered all of the apps that you want.