My M35B idles roughly when first started; I usually boost the revs to just off idle which smooths it right out. It smooths out after it's been running awhile. My tach is off after switching alternators (on the list of things to fix), so I don't know what my idle rpms are . My boat does close to 3 knots at idle in the smooth waters approaching the marina; I usually go to neutral 2 piers before mine and coast the rest of the way. But I don't recall it doing 3+ knots.

Engine idle on the Mk II is typically about 850 rpm, but at that engine speed things tend to vibrate...my cockpit locker cover goes resonant, for example. Smoothness of the engine can be improved by confirming proper engine alignment (it might be; might not) and making sure engine mounts are OK (they probably are).

I tend to set the throttle for smoothness, on my boat around 950 or 1000 rpm. It's OK to shift in and out of gear at that rpm to control speed in close quarters.

Someday I intend to dampen the cockpit cover with rubber pads to silent it, but somehow someday never comes.

You're going to love the boat.

We had some problems like that. In our case, we changed all (3) diesel filters.
Result -> smooth in every RPM.

This engine can run extremly smooth. Took us 6 years to find out.

Is it truly running "rough" or are might you be hearing the "rattle" of the Hurth transmision's damper plate assembly? My 35B sounded like a box-o-rattlesnakes coming down the fairway at idle, (< 1000 though), and it drove me crazy. The noise would stop when I shifted into neutral from idle or throttled up a bit.
My solution to this problem was to replace the damper plate with an aftermarket piece. Solved the rattle.