Any updates Unmicky? I was getting ready to post an almost identical question when I saw your listing.
I just got back from 10 days of working on a Catalina 30 with a Universal 4-30 engine that I inherited. I have limited experience on boats, so this one is the constant learning experience for me. The boats been sitting for a couple of years in Sitka, Alaska. Initially, she wouldn't start - starter would crank and crank the engine, but no go. After a bunch of hunting, turned out the fuel kill slider on the side of the injector pump was stuck in the kill position. Got that sorted out, engine put back together and it started up! Revved up in neutral just fine, could get to max RPMS, no problems. Put it in gear to leave the dock for the first time a huge cloud of black smoke and oily residue came out of the exhaust, much as you described. Managed to get the boat out of the slip and onto the sound a few times, but anytime RPM's climbed over 1800-2000 in gear she started putting out tons of smoke. Also, wouldn't climb over 2200 RPM in either forward or reverse though she would get to 3500 or so in neutral. Like you, in Neutral, no smoke, no problems. In gear, tons of smoke.
Talked with a few people at the docks and the cousin I hired as a "handy man" diesel mechanic (the only professional diesel mechanics in town stated they either had to much work or didn't work on sailboats.) We came up with a handful of possibilities....
1) Growth on the bottom of the boat. While there is some, I doubt this is causing the problem since I got her up to 6.5 knots under sail.
2) Fouled prop or growth on the prop. My only hesitation is that there isn't a bad vibration in gear and I would think that there should be if there was something with the prop. Maybe I'm off base on thinking this? Couldn't visualize this from the dock, and the water up there is to frickin cold to hop in to for a quick peak. Need to either pull the boat this summer or have someone dive on it anyway, so will check the prop at that point.
3) Something in the transmission. Since it only happens under load, maybe the transmission has some issues. I partially suspect this mainly because it's one of the only systems that wasn't looked at.
4) Bad injector. Lots of folks with plenty more experience than me suggest I need the injectors looked at - I don't know enough about all this, but it seems to me that if the injectors were bad, the engine would run rough in neutral and sound rough at idle and through all rpms. Am I wrong on this front?
5) Old Fuel. The fuel in the tank has been sitting for awhile. Unclear on exactly how long. Again though, if this were the problem, I doubt the engine would run well in neutral.
Would really like to hear what worked for you Unmicky as it sounds like very similar problems. Would also be very interested in hearing/learning from other's about the possible causes I've listed and anything else I should be looking at.