misfing engine ??wiring loom??

[marshy01uk]

I own a VW Sharan 1.9TDi 90BHP ANU engine (2000 new model) with misfiring problems. I've owned the Sharan for 5 years and over this time the problem has become steadily worse, it used to be a case of turn off restart and it cleared, no longer the case. As advised I changed the injector wiring loom (Aug 08) and cleared the fault codes (low voltage to 1 and 3) and my car ran like a dream, well for about 6 weeks and the same fault reappeared.
Its been intermittent ever since, I can go a day and its fine before reappearing again, or can go a few weeks without any problems. I have basically been tolerating it but its really getting to me again. Could I be so unlucky to have got a dodgy new wiring loom? Could it be the EGR valve? I just don't buy its the injectors as why would it drive so well for weeks and then go again?
The symptoms? start her up and its like she's running on 3 cylinders, difficult to accelerate until you get up the gears and gather speed but still nowhere as it should be. Its worse when its cold. The misfire symptom can be really bad or quite subtle (tho mostly bad) sometimes when the engine is running well (no symptoms) and idling you can sometimes hear the engine beginning to develop the symptom. i hope this is enough information, I do plan to get it VAG COM'd but would really appreciate any input.
Kind regards
a desperate Sharan driver!!