Compatibility between spytag/spycatcher versions
I am currently working with these tags, so going off experience here. The binding efficiency is not 100% even when the correct versions are mixed e.g. version 2 spytag and version 2 spycatcher. I believe this is the original paper (https://pubs.acs.org/doi/pdf/10.1021/ja910795a) it reported 60 % binding efficiency after an hour (I presume for version 1) and this paper (https://www.pnas.org/content/pnas/109/12/E690.full.pdf) revealed 40 % binding efficiency in the first minute (unclear whether version 1 or 2 but I presume 1).  In terms of between versions I can only speak to a mistake I made once by accidentally mixing version 1 spycatcher with version 2 spytag. There was visible binding that could been seen by SDS-PAGE however, it was very faint and required significant amounts of protein to view (~10 mg/ml). I never did any sort of quantitative measurements on binding efficiency as it was a mistake. But from subsequent correctly run experiments, I could see it was significantly lower so I would always use version 2 with 2 and version 3 with 3 etc as they were designed to have maximum binding efficiencies.