Re: ERUGH!!! Finally!! But....
Whilst I understand that you wanted to commision the guitar straight away, I would have definately taken issue with the shop immediately upon seeing the flaws, before I started modding. Can you replace the original pickups and give them a call?
It seems that many people are unhappy with the quality of their guitar purchases. I feel that if something is bought new, it should be just that. No dings, no marks, no missing trem bushes, no crackling electrics. The shop is your only point of contact with Ibanez, and I am sure that they would have some kind of protocol for defective goods.
I have seen people come into the guitar shop I frequent with really petty stuff about leads, or the fact that their son can't turn on their wah pedal (wasn't standing on it hard enough), they always look at all those issues considerately. Whenever I get a set up, my tech always asks me if it is okay. It always is, but it is good that he asks me. When you have a legitimate issue with something you have bought that is that expensive, I think that you should be on the phone straight away.
I don't wish to preach and I feel genuine sympathy for you, but the only way Ibanez will get better on this is if we are all more selective.