kash75,
You should have started a new thread with this issue.
Anyway... it sounds like your situation includes everything that you are not supposed to do.
Even if you are able to find the right filter arrangement, as soon as you have it, it will begin to degrade, albeit slowly. However, with time and changing conditions, sooner or later, the problem will reoccur. All it takes is for conditions to change... and they will.
You would do best to bite-the-big-one (bullet) and re-route the thermocouple wires in the accepted manner. That will, at least, provide a standard and reasonable basic environment for those signals.
That effort, in itself, will eliminate a large portion of the problems. Then, if necessary, you can apply minor filtering.
There are Dip-Switch controlled (selectable) capacitors out there. You might consider one of those for the minor filtering rather than fooling around with a handful of discrete capacitors.