I'll try to answer for everything.

1) Points are linked in the algorithm configuration tables by using the F7 key then selecting which point it should be looking at.
2) Pump enables are usually either discrete inputs from outside the controller, a network point from another CCN controller (usually using BEST++), or from a time clock algorithm.
3) Both NST - V and ComfortView can completely program the 6400s and 1600s.
4) A full copy of ComfortView or NST - V, with key, from a Carrier distributor usually is much more than $500.
5) For more information download both the 6400 and BEST++ programming guides from carrier.com, put together they're almost 1000 pages, but they tell you everything about every function in a 6400.