Based on your descriptions of the plays, I'd rule as follows:
Play 1---Type A obstruction. The fielder had the ball and was making a play on R2 when the obstruction occurred. Immediate dead ball, and R2 awarded 3B with BR getting 1B.
I'd need to be certain it was obstruction to call it, though. If I were in C position and had my back turned and did not see the contact occur, I would not rule obstruction on the "remnants" of the contact. A smart R2 may have veered into F6 trying to bait the call---knowing he'd likely be out at 3rd anyway. This call should most likely be made by PU who is looking at the play.
It's not obstruction until ruled obstruction, and if I'm PU seeing the play beat R2 that bad, then CSFP tells me it's very likely incidental contact vs. obstruction if I'm making the call. Either that, or type B (the contact occurred before F5 began making a play) and my "umpire judgment" tells me I protect him to the base I thought he'd safely obtain had obstruction not occurred---which is "none".......UNLESS further post obstruction evidence warrants it. In your actual play, the offense likely judged it the same way, and that's why you received little grief regarding your "out" call.
Play 2---Type A obstruction with BR awarded 1B due to obstructing the runner on a fair batted ball before runner reaches 1B.
Play 3---This is a much more difficult call.
NAPBL 4.22 (now the PBUC) states:
Official Rule 7.06(a) deals with cases when the runner is obstructed while a play is
being made on him [NAPBL emphasis]. Examples of this type of obstruction include:
1. Runner is obstructed during a rundown.
2. Runner is obstructed as a fielder is making a direct throw to a base in an attempt to retire that runner.
3. Batter-runner is obstructed before reaching first base on a ground ball to an infielder [NAPBL emphasis].
4. Any other example where a play is being made directly on the runner at the moment he is obstructed.
If you have judged the runner is not legitimately attempting to advance to 3B, how could the throw be an attempt to retire him?
In your play, if I judged there was no legitimate attempt to advance, then I would also judge this as Type B obstruction since no play was being made directly on him at the time of the obstruction, even if the ball were in the air toward 3B. Type B is umpire judgment, and I would protect the runner safely back to 2B, but not feel compelled to award the runner 3B---as you question.
If I judged he was legitimately attempting advance while obstructed
and while being played upon, then I would kill the play and award him 3B even if I thought he had no reasonable chance of being safe at 3B. That's the penalty for Type A obstruction.
Here is a very similar play from J/R with their ruling:
R1, hit and run. The batter hits a line drive base hit at the left fielder. Rounding second, R1 must alter his stride to avoid the shortstop, and he stumbles- obstruction. The left fielder throws behind R1, who is now returning to second, and he is tagged: the return of R1 is protected. Indeed, the umpire must determine if he chose to return, or if the obstruction caused him to return when acquiring third was his intention, and was reasonably possible.
Note that in the J/R play the obstruction occurred before the play was being made on the runner returning to 2B. That causes the obstruction to be Type B---umpires judgment to nullify the act of obstruction.
Had the runner been obstructed while the play was being made to 2nd and during his return there, it would be Type A obstruction with the ball immediately becoming dead and R1 being awarded 3B (by rule-one base minimum).
Also note in J/R play that had the throw been behind the runner, but the umpire judged R1 as having legitimately advancing to 3B when obstructed and as having a reasonable chance of acquiring it, he could (and likely should) award 3B to R1.
With Type A obstruction you MUST award at least one base; with Type B obstruction, you use "umpire judgment" to nullify the act of obstruction---which typically means you protect him to the base he'd most likely obtain safely. There is nothing written in the rule that says you MUST protect him anywhere, although some other posters interpret those words into wording of the rule.
Just my opinion,
Freix