What date did you send them the CoC? it shouldn't be talking them longer than a 6-8wks to register it. Also did you get an email receipt..? if it were me I would refer them to that receipt if you get any charges.
And talking of TFL, I have been speaking to the ULEZ dept. today with regard to a 2007 FZ1 that was registered on the 11th of May (so 14 business days before the threshold of 1st of June 2007) and they are now saying that via their website I can send them a scan/copy the logbook. But this will only work if section V.1, V.2 & V.3 (CO, HCL & NOx) are populated. So I have asked Yamaha why my logbook is missing this info, seeing's as Euro3 came in to force in 2002 for motorcycles. Basically I would prefer NOT to pay the £75 for a CoC if it becomes clear the/original registrant didn't send the info to the DVLA from the get go.