1. Rev C and Rev D are essentially identical w/regard to this issue. However, Rev D solves this better by using LVC-series chips for U1-U3 (and in other places, too).
2. U3's connection to the processor (U6) is at U3's _inputs_. Therefore it doesn't matter (too much) if you route analog signals to P6[5..3] -- they will appear on U6's analog inputs and on U3's digital inputs, but who cares? At most, you will suffer from some extra current draw by U3.
3. Handshaking was put on P6 because you can always use a remote ADC -- that's trivial. What you can't easily do is move _timer_ operations or interrupt-on-change or byte-wide ports off-chip -- performance suffers horribly in all those cases. So we made a choice to put the (optional) handshaking lines on P6. In hindsight, I probably should have put them on P4 or P5. In Rev D, they can be done by alternate ports with future FPMs that have more than 48 I/O pins.
4. Handshaking is useful when you're running at very high baud rates ... at slower baud rates, software handshaking (if used at all) should be OK.
So, I suggest you remove R10, R11, R12, R75, R76 & R77. This completely disconnects the various handshaking signals from the MHX. A[2..0] will be completely free from any analog interference, and A7 is a direct connect anyway. (Note that A7 is also a DAC12 output on some MSP430s). Whatever drives A[5..3] will also drive 1A2, 1A3 & 1A4 on U3 -- you will see some excess current draw, since those are digital inputs. But it shouldn't be a huge problem.
You can also remove R2, R3, R4, R6, R7 & R8 as well.
Please note that the notes on the schematics are incorrect -- it's R3, R4, R7, R8, R11, R12, R76 & R77 that are normally not fitted. So you only need to remove 2 (or 4, for USB) resistors.
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