For which users? Need to track this down and see what is different about their permissions.
You need to realize that spam mitigation is running in the background. xenForo implemented spam measures to combat spam. So, your members are, to the software - unknown. You'll get false positives here and there. Turning it off will put more work for your other admins and mods.
1. VB had a less functional design when viewing on a device hence the need for something like tapatalk. XF should be a lot better in that regard. There are a couple features I think TT users like but it's been a common theme to drop TT on forum admin boards for a number of reasons.
2. should be able to update old threads if not let us know i'll we'll look into it.
I'll focus, and respond to #1. First of all, while xenForo 2.1 does have features that users loved about Tapatalk, it's not nearly as much as you'd suspect. People love the "native app" feel of Tapatalk, so - and mysiteguy can confirm what I said. It's not always a good idea to remove Tapatalk, because you're still dealing with users. Those users want Tapatalk installed. You have two ways of mobile viewing. Some people like the mobile view of the forums, some people like the Tapatalk "native app" feel. TAZ and other forums think to drop Tapatalk, but you're actually missing out, when you do. Tapatalk is actually a network and a search engine. You want new users? You'll need Tapatalk. Especially if you plan to put your "app" on Android and Apple stores. On top of this, google favors mobile sites like Tapatalk, so if you want the traffic to blow up, keep Tapatalk installed at all times, even if you have to re-install it onto a new platform (XF2).
Congratulations on the conversion, by the way!