It sounds like you have the skills needed to tackle such a job.
Although I don't think it's the exhaust mixing elbow, it might be wise to check anyway to see if it's clogged. When mine (mixing elbow and manifold water jacket on Yanmar) clogged by carbon buildup, the engine overheated at anything much over idle. However, there were no new noises which makes me think this isn't your problem.
From the very limited experience I've had... The most "high tech" part of a diesel is the fuel pumps and injectors. The rest should be simular to a gas engine.
Breaking out my crystal ball... I see the purchase of a repair manual in your future (unless you already have one).
To answer your question... You don't sound like you're nuts. I don't think I have as much mechanical knowledge/experience as you do; and I wouldn't be afraid of pulling the top end off and checking for excessive wear, or even pulling the engine and doing a rebuild.
I hope it turns out to be something easy.
Skipper, J/36 "Zero Tolerance"