Once a battery goes severely flat it is as good as gone for that car IMO especially on a diesel which will naturally give the starter motor a harder time. It certainly was for mine when I changed it (the ASR and ABS light would come up as failures on some cold mornings). Now I get a clean start every time (battery that came off was an ill fitting Lucas 3 year Premium battery that was a little old and came up as a slight duffer on the drop test).
Regarding your charging issue I find for peace of mine you are best off disconnecting the negative lead. That way you can also do a poor man's drop test on the car and see if your battery really is getting past it.
It's a shame you are not closer as I would have helped you with obtaining a correctly sized battery a little cheaper than usual.
I am not sure if Euro Car Parts are doing their discounts but they certainly ensured that you got a good battery at a reasonable price (code was battery15).
Failing that, mine is starting fine on a Bosch Silver S5 battery of the 096 sized variety, and it fits perfectly.