R.E. Lee decided he wanted to run for president? How would that have played out? What would the process look like? Further, let's suppose his oath as an officer was to "preserve, protect, and defend" the constitution, as the current presidential oath does.

Would he have to be convicted in criminal court of insurrection to be kept off the ballot? Would congress have to pass a resolution stating that he was not eligible? One house or both? Would a federal court have to rule that? The constitution is silent on all of this.

Why shouldn't individual states be allowed to keep him off the ballot? Many candidates appear on some but not all state ballots. There are individual requirements and processes for gathering signatures, etc. Why can't they have differing requirements for qualifying as "not an insurrectionist".

Would southerners argue that he was a freedom fighter, not an insurrectionist, so he should not be disqualified?
Would they say that the wording of his oath meant the 14th did not apply to him?
Would southern states allow him on the ballot and northern states not?