Actually MaxBranchDepth doesn't do anything in MCW (branch depth is defined in Branch() itself and is passed from parent to child branches with a -1 modifier until it reaches 0 which is the end of the branch).
Be aware btw there has been a slight change in branch syntax for MCW meaning that you will have to edit all your BO3's branches for use with MCW. This should be pretty easy to do though, if your branches use only rotation North you can probably do it with some simple find/replace in notepad++.
In any case, see the MCW thread for documentation on branch syntax in MCW and post there if you need any help with branches. I actually suggest you experiment first with making a very very simple branching BO3 from scratch with MCW, I think you'll love the new branching features (IsBranchEnding parameter, automatic collision detection & branch rollbacks, inheritable branch depth, infinite branch depth, all kinds of optimisations etc)! Ask me any questions you like. It would be really useful to have someone do a little test of the branching features in MCW, you're probably one of the most experienced branching BO3 builders so you'd be the ideal candidate :).
And if you want to see some really advanced MCW branching stuff, load up the jungletempledungeon and graveyardtomb BO3's that are packaged with MCW and TCEE (you can load this TCEE preset "Saves/PG85 Islands/SingleBO3UnderWaterCityWithRandomGenDungeon.xml"), you only have to change a few numbers in the right place (worldborderradius and branch depth in BO3, just ask me) and the temple and its dungeons can be made to grow to any size, as far as the eye can see :).