Deanna, your first two examples have an incorrect initial setup. As noted in another thread, seeing the full history makes it much easier to answer the questions. Also, the natural pairing for the odd man is to have the bottom player in the upper score group play the top player in the lower score group, and your listed round two pairings did not do that.
As a side note, the pairing ranges are greater than the normal ranges the USCF rulebook was written for, so adjustments to the 200-point and 80-point limits may be in order.
In A, the round one pairings would have been (colors unknown)
4213 (1) - 2855 (0)
3171 (0) - 2065 (1)
2739 (0) - 1892 (1)
In any case the natural pairings for round two would be
4213 - 2065 (top two 1s)
1892 - 3171 (bottom 1 vs top 0)
2855 - 2739 (bottom two 0s)
If you opt for Harkness pairings (drop the middle) then the raw
4213 - 1892
2065 - 3171
2855 - 2739
would be changed (to avoid the repetition on board two) to
4213 - 1892
2065 - 2855
3171 - 2739
In your second example the first round would have been
4055 (0) - 2329 (1)
3147 (1) - 2088 (0)
2913 (0) - 1949 (1)
The natural round two pairings would are
3147 - 2329
1949 - 4055
2913 - 2088
Harkness would be modified to
3147 - 1949
2329 - 2913
4055 - 2088
Your third example is incomplete. If I make the assumption that you really meant round 2 (since only three points have been awarded so far in the tournament) then I run into a problem in that E and F should have played each other in round one and thus should not both have zero points. The only possibility I can see is that the round one pairings were:
3322 (1) - 2701 (0)
2956 (1) - 1981 (0)
1997 (1) - 1000 (0) (the 1000 was originally going to have a bye, and then after the round had started the 1997 player showed up to play)
The natural round 2 pairings would be
3322 - 2956
1997 - 2701
1981 - 1000