How would I format this sentence, it feels like a run on.?

Your question is a run-on. 

A sentence expresses a complete thought.  Your question expresses two complete thoughts, making it a run-on sentence.

 It should be:  How would I format this sentence.  It feels like a run-on.

This is long but correct:

"I had applied to this job four months ago with the assumption that it would be a breeze, and as wrong as I was, I undoubtedly made the right decision".

There's nothing wrong with this sentence except for the use of the word "to" instead of the word "for". It would be better if you said I had applied for this job.......

It looks fine to me, but, since it concerns you, an easy fix is to divide it (into two). Here is one option: I applied for the job 4 months ago, assuming it would be a breeze. While my assumption was wrong, I undoubtedly made the right decision.

It’s fine. It’s a compound complex sentence.

It's not a run on. It has commas in the right places. However, it might not be very impressive to the recruiters if this is part of a new job application. Admit that you made a mistake in taking the application process too lightly.