I've been running a pulley kit for about a year and half, ran dynos when I started, ran ...
I've been running a pulley kit for about a year and half, ran dynos when I started, ran dynos as recently as a few months ago and I see no deterioration in power and I have the stock ECU, same on friends coupes with a pulley kit (even though it's not the same pulley kit as mine). Same with Linh on the R170 forum who has been running a pulley on his 1999 SLK230 for about 40K miles with no reduction in power and he did dyno runs at first and then a year later, same output. Linh sells a kit to go with the pulley on the older SLK's that includes some stuff to make it right like a different fuel pressure regulator, cooler spark plugs and a MAF sensor relocation kit. Yes, you can compensate and fix this with ECU programming but the that's a matter of choice. This is not needed on the new SLK's or C230K 2.3L motors though.
Can't wait to see what improvement you get with both, the pulley and the chip on your C-Coupe.
If you were right about the power going back to stock then I would disconnect the battery for 1/2 hour the ECU will be reset and your power would return if what you say is true, if it doesn't, it's not the ECU. Keep in mind that on a car that old the key sensors like O2, MAF and MAP are getting dirty and weak and may not be reading as accurately as when new although not bad enough to trigger a check engine light and you can have carbon buildup over the years that causes pinging that would require higher octane fuel.