It's very unfortunate in the circumstances that the PCN was issued in Scotland, in the rest of the UK we could easily help you reset the PCN. In any event don't worry about a CCJ, no penalty charge notice can result in one of those.
However unless you want to take out a judicial review against the Scottish Government for breaching the Human Rights Act 1998, there is nothing you can do about the Charge Certificate because the Scottish legislation goes not allow you to make any sort of appeal in these circumstances.
There is no right to any sort of legal redress in these circumstances and there is no court or tribunal you can turn to. This is really something you'll have to take up with your MSP, or you could email those responsible for this area of policy at the Scottish Government i.e. Fred.O'Hara@transport.gov.scot / 0141 272 7293 (but he's previously made it clear he doesn't care) and Sharon.Wood@transport.gov.scot (who did seem to care but then said it wasn't her area of responsibility any more).
As far your charge certificate goes, you can write to the council and explain the circumstances, but if they insist you have to pay the full amount there's basically nothing you can do (apart from the judicial review option mentioned above), so you'll just have to pay.
As for why this breaches the Human Rights Act 1998, that is because Article 6 says:
In the determination of his civil rights and obligations or of any criminal charge against him, everyone is entitled to a fair and public hearing within a reasonable time by an independent and impartial tribunal established by law.
However in the determination of your rights in respect of the charge certificate, you're not entitled to any hearing before anyone at all.
Sorry that this sucks, but it is what it is. I think a judicial review could be won, but that would be a lot of effort to fight.