"Is running across the banks on the South side the smarter way to go ?"
I'd have to plot it but I think it would be shorter than going over the top or around the bottom of the T&Cs. It's shallow but I did it in a boat that drew 5 ft. so it shouldn't be a problem for you. But being shallow it can get choppy.
"How is the water on the North East side of the Dominican Republic ?"
You will be heading into the easterly trade winds so it can be rough with a big swell.
"How's the water typically running from the DM over to Puerto Rico ?"
The Mona Passage can be a bear. But if you stay above it or pick the right time to cross it, it can be settled.
Pick up a copy of: " The Gentleman's Guide to Passages South by Bruce Van Sant"
Now it's written for sailboats and slower power boats but it will give you a very good idea on the weather patterns for those areas.
As far as weather routing goes, look at Chris Parkers "The Caribbean Weather Center's Daily SSB Weather Net" http://www.caribwx.com/ssb.html
While he broadcasts on SSB, I think you can call in for a personalized forecast. Or get it via Email. I'd bet he'd get a kick out of how short a weather window you'd need traveling at 60 mph.
If you want to do forecasting yourselves look at using OCENS weather software via your SAT phone. http://www.ocens.com/index.htm
And go with an Iridium phone.
Or do both. And there are other weather routers you could use as well.
Looking for any crew?