Right now MainStage 3 is not compatible with Mobius because the new version of MainStage/Logic will only work with 64-bit plug-ins. Jeff is already working it though so maybe by the time you incorporate a host then Mobius will be 64-bit.
can't you just run mainstage in 32-bit mode? (right-click, get info, select open in 32-bit mode)
anyhow, welcome to the machine Bill. I'll echo the advice to check out Bidule. Not only can you sync all your effects to your loops, you can also have multiple sync sources and easily divide or multiply the clock as required. I haven't spent a lot of time with Live, but my impression is that if you're not using pre-recorded material, it's overkill. Mainstage is a great alternative (decent effects and instruments for a ridiculously low price).
However, the boxes and cables interface of bidule should be really straightforward for someone coming from a hardware setup, and you could actually try to mirror the signal flow of your current pedalboards... Also, if you need scripting beyond what a plugin allows, you can use bidule to extend the functionality of your plugins (setup a patch that sends a bunch of midi signals to control your plugin). It's also much cheaper than Live and if you ever get Live, Bidule can be used within it as a VST or AU or along side with Rewire.
Of course, ask any questions as they arise and I'd be happy to help you with any scripting you need