Duane - 
A few issues: 
1)The low side of each half-bridge can be connected to the same sense resistor. See http://www.irf.com/technical-info/refdesigns/irmd2336dj.pdf page 7. You'll see how all three half-bridges are connected to the Rshunt, which is used to develop a current feedback fed to the Itrip input.
2)The current sense resistors are way way way too large. We're trying to push several A thru them, which means a voltage drop of several volts. Better to use small value sense resistors along with an op amp buffer to achieve the appropriate voltage (5V at maximum current).
3)To the extent possible, the motor ground return, analog ground return (for the op-amps and any other analog signals) and the logic ground returns (with all the high frequency clock noise) should be kept seperate, and only join together at one point, preferably near the power input terminals on the board. This way the logic and analog grounds aren't carrying the motor return currents (which are large). I like to denote this in the schematic with seperate grounds, with an explicit tie. It becomes tricky at layout time, because you might need to grab ground at one of the board and end up using power ground for logic ground. But keeping them seperate will avoid lots of problems downstream.
4)Its not clear where the logic-side supply voltage for the half-bridge drivers is being derived. I am assuming it is 5V from the regulator.
5)If you haven't read it, take a look at app note http://www.irf.com/technical-info/appnotes/an-978.pdf from IR. Lots of good info on component selection and layout.
Hans Thomas 
AUV Supervisor, Division of Marine Operations 
Monterey Bay Aquarium Research Institute 
831-775-1976 (landline) 
831-869-5693 (mobile) 
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