Toaster,
I know exactly what you mean. I too learnt to fly three axis microlights at a grass strip outside controlled airspace and received little practical instruction in the use of flight information services or ATC. After getting my PPL I went on to get my FRTOL on a two day course. It then dawned on me that despite this my practical training and understanding of flight services was sadly lacking. I read CAP413 again and again but remained nervous of putting it all into practice.
My best advice is to find an instructor who will give you "in the air" tuition so you gain confidence in using flight information services and flying in Class D. It will cost little compared to what it has cost to get your PPL.
This is not your fault, it's a fault of your training and at the time you knew no different and your instructor didn't see it. Good on you for realising it and asking how to sort it out.