Well... this was specifically in reference to my comment about using cutadapt. That is, if you run cutadapt to remove the primers, your sequences will be shorter. So you'd have to re-visualize them.
Trimming the 5' ends will not have an effect on the merging process, specifically. It is the quality and overlap of the 3' ends that matter.
As long as the quality is good, and there is enough over-lap to merge the reads, being "too long" or "too short" won't matter.
Did you try the specific truncation values I suggested? Especially the fw: 268 with rev: 211? There can be large differences just shifting a few bases over.
-Mike