insert size pre and post trimming
It's not an unreasonable approach. rMATs is rather picky about its input, but it seems you've noticed that.
rMATs can't handle trimmed reads. It also can't handle soft-clipped reads. You might as well not trim. You'll get a lower alignment rate, but your only other choice would be to either exclude the trimmed reads or trim everything down to the same length.
You have a mixture of RF and FR alignments and the plotting script can't handle that.
Assuming you mean the read length distribution, it's actually shifted to the left, not the right. You had a single length before and a long left tail after trimming.