Hi Jaime,
I completely agree that a night off (or two), maybe a couple of stella's and doing something completely different is a huge help when things start to look a bit gloomy. You've worked your balls off on this car recently, so have a break from it.
When you return however, I would say that
1) The alternator must have some way of coming out, without engine removal. BMW are stupid, but not that stupid (one would hope!). Does your software give any indications as to the procedure?
2) The injector pump. you're right that, if you don't have experience in this area, you can cause more trouble than it's worth, by adjusting. I've done the job on Peugeots using the book of lies, but I certainly wouldn't take on the task light heartedly of doing this on a TD omega, specially with a BMW lump. I guess in answer to your question, the only way that the problem could be caused, is if the pump on the donor engine is different to the original, and requires a different set of ECU values/instructions to make the engine perform? I may be way off scale, but I know little about the modern TD.
3) I read that Omegatoy filled the diesel filter with diesel, and it started and ran on all six. Does it now run on all six using the fuel from your tank - or is there still an issue with delivery?
4) Is the Tech2 reporting any present engine management codes?
5) Is the air intake/turbo etc all connected securely and happily?
6) (and totally no offence intended here) - How much do you trust the seller that the engine is good?