to me what you're describing is simply an engine that needs to be retimed, from the beginning: flywheel at exactly TDC, cam sprocket free to rotate, camshaft locked and shimmed as required, belt at the correct tension, pump with locking pin installed.Having said that, if you found the pump timing (using TDC on the flywheel as your reference) to be correct then my guess is that your cold-start problems probably lie elsewhere... in my experience diesels are not particularly sensitive to small errors in valve timing. How's your glow plug system working ? Got good compression ?
I'm hoping to replace the timing belt next weekend. I'll time it directly to the piston through the injector hole. I'll let everyone know what I find.
Check to see if there is any wobble in the crank pulley when the engine is running. If it is nice and straight then it SHOULD be ok. The only real way to check it is to pull off the pulleys and timing belt gear and look for wear on the key and surfaces.