Q: What are my chances of winning this case?
A: Zero. All the government has to do is show that you ran the red light and that you didn't show up for court. Your intentions are irrelevant (as are the facts in the first part of your post).
Q; Don't I have the right to be tried on any offense within a reasonable amount of time?
A: Speedy trial doesn't apply to traffic.
Q: Eventhough I am positive that I did not run the red light, in the worst case scenerio, even if I am guilty, isn't 14 monthes too much to correct a traffic voilation?
Q: I am thinking of requesting the court clerk to testify that there had been an error in entering the citation in the court records (not sure if she will agree to testify or not).
A: That will never happen; you can, however, ask the judge to take judicial notice of the court's own records (whatever the records say).
Q: Also, I can show phone records that I did call them up even on the day of the court date.
A: That proves nothing.
Q: What else can I point out to prove my innocence?
A: You're not innocent.
There are two rules for success:
(1) Never tell everything you know.