I have been enjoying my Krank Rev Jr. Pro. I put some better preamp tubes in it and it made a big difference.

I noticed that it's a 2x 6L6 power section... yet only 20w. Probably the only difference between this version and the 50w version is the output transformer.

Part of my deal with this amp is that the reason I wanted a low power tube head was to drive/saturate the power section at lower volume than on a big amp. I am pretty sure that on this guy it just starts to transformer clip when really driven.

Anyone know what a mod like this might involve?
Umm...transformer clip? Sorry man, a lot more goes into the output rating than the transformer. In fact, the ratings that amps receive are mostly just arbitrary. I'd be amazed if many production tube amps were within 20 or 30% of their "RMS" output ratings.

As far as replacing the transformer goes, I wouldn't bother. There can't be a large enough market for the transformers for those amps for it to be vaguely affordable. If you want the full size rev sound, get a full size rev.
I don't give a shit if you listen to me or not
Find the schematics for both versions and we'll talk. The transformer probably isn't the only difference.