I have lots of apps on my iPad and I want to copy them to my PC, usually I'd just click transfer purchased in iTunes but now it's not working. I want to backup and restore my iPad because I've been having some issues. iFunBox isn't working either
Transfer purchases was actually disabled in iOS 9. Apple disabled it because there are many different variants of an app from the App Store. This means that an app that was on an iPad Air that was then transferred to a PC can't be used on an iPhone or an iPad Mini.
A thread was posted here about why it was disabled and goes into more detail.
If you want to put all your data onto a new iPad, just backup your old iPad and restore as a backup on a new iPad.