An alternative for those that can't find the manually sync apps option would be to
Plug iPad into computer, open iTunes and sync iPad. Usually they sync automatically and if you haven't don't it for a while it will take half an hour or so. That's step one to get all the apps you own onto iTunes on your computer.
Then unplug the iPad and just manually delete all the apps you don't want on the iPad at the moment. Before you do that please do this!
While the iPad is NOT connected to the computer scroll through the apps in iTunes and make sure you have lots! Just check that step 1 was successful by randomly looking for apps you know you own. Then you can delete without worry
This works for iPhones and iPods as well same instructions for all
The cloud being full I have no experience with sorry. I decided to turn my cloud off as we have 5 devises under the one name ( I only pay for apps once and I can use them on all five devises, 3 iPads, one iPhone and a iPod.) if I purchase a book for me I don't want it to automatically sync to my children's iPads. Especially if I decide to purchase 50 shades of grey
if I activated my cloud it would sync all the books to all the devises and the kids would get some surprises
and all the iPads would be full in no time!
I assume you could delete the items in your cloud through iTunes once they are synced to all the devises I imagine this would be a good idea. She only problem would be if you wanted to keep active bookmarks in your books...ie read a book chapter on your iPhone and then continue reading the same books t home on the iPad later. Hmmm I could read up on it. It would be good to know if I can restrict the clouds options....