I assume the motor is in the water and not on muffs.....
There are several things that can cause roughness but it's not all that easy to identify the specific cause. I have a few thoughts; if your motor idles at 600 revs, that may be too low but don't adjust right now.
The fact that is runs smoothly at 1200 is a clue because that is where all cylinders kick in. That can eliminate 2 cylinders as the culprits. I am not 100% sure what cylinders deactivate on the HDPI. On mine I think the lower two deactivate.
So now we look at what can cause the roughness in those 4 cylinders.
The first test is to removed the plug wires on the working cylinders, one at a time and see if the motor gets rougher. It should for each cyl. If you pull a plug wire and the motor doesn't get rougher, that cylinder is having a problem, probably spark or gas.
A cylinder could be getting spark but intermittent gas. In the first case a coil could be bad. In the latter case an injector could be sticking, clogged or not working at all. If you get a plug tester that connects inline with a plug wire and had a lamp that flashes, you can look for consistent spark at idle. You can get a really cheap tester at Harbor Freight.
It is also possible to kind of check injectors by holding a screwdriver on the injector housing and pressing your ear on the other end of the screwdriver. They also see stethoscopes with pointed ends to do the same thing. You should hear a regular clicking as the injector gets triggered.
If you have a bad coil, it is more obvious at lower speeds since 1 out of 4 cyls is not working. As you rev up, that becomes one out of six and the only symptom might be a drop in WOT revs.
So do the 'pull the plug wires" test, and go from there. I suggest that you loosen the wire at the plug first and lightly insert it. Then use an insulated pliers or the like to pull the cable with the motor running. That will reduce the chance of you getting zapped
Good luck.