BRD under malicious contact with the chart that says if the runner scores and then the runner commits malicious contact to not count the run on a force but to count it on a non force play.

Where is the rule/case interpetation for this? Fed 3-3-1n says the runner is not declared if he has scored thus the runs scores. To me if he is not out then the run has to count. Case book says 2 outs and the malicious contact is by R1 (runner on first) making malicious contact before he gets to second (force still on). In that case you do not count the run.

In chart if the runner has scored then by definition the force is off when he touched the plate and then if he makes the contact then count the run and dump him.

Am I missing something in my thinking on this? Or am I overlooking a rule that say different from what I am seeing?

It's a FPSR violation so the run doesn't count, the BR is also declared out and all other runners return. See 8.4.2Y

Ok I have no problem with that as that is a typical FPSR, but what about the runner who crosses home and is not having a play made on him. Say he just bowls over the catcher who is just standing behind home?
Also the play you mentioned the force is not removed there, lease the way I am reading it, as R3 still had not scored when he initiated the malicious contact.

Check out the citations given in the BRD, Section 319.

3-3-1n: Runner maliciously crashes into a fielder: "The umpire shall eject the offender from the game. The ejected player is declared out <i>unless he has already scored</i>." [my emphasis] So he is NEVER out if he has scored

EXCEPT

If he violates 8-4-2b: "A runner is out if he does not slide and causes illegal contact." Penalty: "On a force-play slide with less than two outs, the runner is declared out."

It's unfortunate that 8.4.2Y (a) and (b) both occur with the bases loaded. Try this play, though:

B1 and F2 exchange words on an inside pitch that almost nicks B1. He then doubles and intends to score on a single to right. He does make the plate [not a force play, so there can be no violation of FPSR] and after scoring maliciously contacts the catcher. He is ejected. But his run scores.

What may be confusing you is there are TWO rules in play: FPSR and Malicious contact.