This is most likely the squish.
If someone built that top end for you, they probably used too thick a base gasket reducing the compression ratio. The cylinder head could sit be marginally higher than what it was before, meaning the squish is off.
I am not saying this definitely the case, but would explain why you'd lose bottom end. I am not sure about the heavier piston, sounds like a cop out, but if a different dome was used, different profile, then same answer. The squish is affected.
A vast majority of power on a two stroke is made in the head, so it could be that the squish band isn't correct. This is a very simple and easy thing to fix and measure. All that is needed is a set of vernier calipers and some 1.2mm thick solder wire, with a dab of grease to stop it falling into the bottom end.
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Could be this, especially as you say, it was fine before the top end rebuild, noticeable after.
I once went from the stock 3MB00 cylinder, to the TZR R Belgarda 3MB00P which has a raised exhaust port by 1mm and as a result, greater over-rev (ideal for the TZR) loss of bottom end (less ideal for the DTR).
I went from lifting that front end up with ease (no small feat on my heavier setup) to having to work for it.
Now I run a ported Athena 170cc kit and I love it for the low-rev grunt. I have my RS125 which is lightening fast so I enjoy both aspects now :)
I am by no means an expert and please someone else chime in and correct me, but based on what you've just articulated, this could explain it.
