Hi Szymon
can you share a few pictures of your setup from different angles including your guidescope setup?
I'm not sure I agree with your assessment. It looks like you have significant issues on both axes.
Looking at your 3h45min run, your Dec is actually higher than RA.
On the second shorter 1h45m run it's not that much different, although RA is a touch higher.
Your min moves are a higher in dec, but even with a backlash compensation of 2 seconds, it's taking dozens of guide pulses before the axis responds:

So on your Dec, i'd say there's a lot of mechanical backlash that you need to address. you didn't have any opposite side of pier guiding, so i can't comment if it's impacted by balance.
It would help to upgrade to the latest release and follow your calibration (via the calibration assistant) with a guiding assistant run. It will help measure backlash there
On RA, the primary PE is really high, nearly 100" peak to peak. PPEC can help some (and you have the right period length, although I would disable auto adjust period) but the amount is just too large.
You will need mount-based PE to help here (or possibly some mechanical adjustments as well)
On top of all that, it looks to me like your axes have some bleed between them, note the dec has a similar sinusoidal pattern that matches RA
it's possible the magnitude of your PE is influencing this, but it may also be your guiding setup is rotating slightly and may be contributing to this (and why I asked for some pictures).
Brian