If I'm reading your posts correctly, you matched into a categorical IM position, ended up with a medical LOA, completed your intern year off cycle, but required some sort of remediation at the end, which you completed.
Here's what we need to know:
1. Will they say that you completed the intern year, and are ready for a PGY-2 position?
2. If so, why did your PD not give you one? If the answer is "not a good fit", both of you need to tell the same story why.
3. What was this late remediation? Are we certain it is "fixed"?
Answers to some of your questions:
1. If you completed a PGY-1 successfully, it's unlikely (but not impossible) that a program will give you another PGY-1.
2. You can look around for a PGY-2 opening. If your PD is willing to support you, they can help by contacting other programs. There is no central list -- you simply have to contact programs in which you are interested.
3. In SOAP you could apply for a PGY-1 in a new field, or a PGY-2 "Advanced (A)" position (which would start July 2017), or a PGY-2 "Reserved (R)" position (which would start July 2016). You only get 30 applications, so you need to think about this and choose carefully.
4. You need a letter from your PD uploaded in ERAS ready for SOAP.