When doing the carb loading part of the plan can you spread the carb part over 2-3 meals (say lunch and dinner) rather than the last 1-2 meals of the day?

You CAN do whatever you please. But the program calls for the carb-load to be the last 1-2 meals of the day, so if you do not get the results you want, look to this departure as a possible reason.

On a carb loading day, if your last 2 meals are the pre and post workout meals what do you eat? Can you eat a high carb low protein sports bar or drink? Are these too high with simple carbs? 

You are working-out at a hormonally incorrect time of day. (see Ask Rob - Timing of Resistance Training)

I have heard that a high protein diet leads to a shift of the body's pH towards acid conditions (acidosis) and that this shift is not healthy. Is this true for the NHE Eating Plan?

No.