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What do I do with the other 2 ports? I believe they're B and C. Do I just leave them out?

You're going to have to give more context to this.

I bought a socketed ECU with the conversion harness that only contains 3 ports while the ECU itself has 5. I'm assuming the 2 ports that don't fit in the harness because their are no associated PINs are covered by the other 3. I'm literally just trying to figure out how to plug the thing in.

The Rywire conversion harness? Port C and D are for automatic transmission, so they're not used on the conversion harness.

Are you planning to take the setup to one of our dealers?

Sounds like you were sold a Auto ECU, which is not a problem at all. The harness is ONLY made for a manual car so you will have C and D without a plug in it.

So this being said. What do I do with the remaining two ports on my automatic tranny? Or should I have simply removed the conversion harness and plugged directly into the car with all five pins?

I don't understand your question. If you purchased this for an automatic then you didn't specify that to a dealer. The conversion harness (Which we do not make) is for manual setups. You'd need to modify your factory automatic wiring (C/D) if you plan to use an Automatic transmission.

I specified with Xenocron that I wanted the conversion harness with an automatic PND ECU. There was no other specification option available during the purchasing process. I'll re-pin and let you know how it goes.

Oh, I see. You didn't actually speak with them. I'll get them to specifically mention that it's a harness for MT.