For taxes owed, as long as it is being rectified as in being paid, you are fine.
In your case, you stated that you are on a payment plan so you are ok there.
For taxes return documentation, the requirement is "1040 and supporting documents" or "tax transcript" NOT both.
In your case, you filed for an extension, so it was now due in October, then you filed before October deadline. So again you are ok. Just take the return and supporting documents. The key is when you filed, not when it is processed.
There are people in worse situations than yours. I don't see any reason for concern