Failure to timely submit for PPA determination letter - correction?

DB plan failed to adopt a good faith PPA amendment or a 436 amendment.  Also, the plan adopted its PPA restatement late and did not submit the plan for a PPA determination letter.  The plan received a favorable EGTRRA letter after entering a Closing Agreement with IRS regarding other late amendments (which were ultimately adopted under the Closing Agreement).

I am having trouble finding any guidance on how to submit these failures for coorection through VCP.  I know I can correct the nonamender failure as to the 436 amendment.  However, given that the plan has been restated for PPA, do I need to correct the good faith PPA-non-amender failure - or would that failure be considered "corrected" by the (late) PPA restatement?  Should I just submit the 436 non-amender and the late PPA restatement as non-amender failures and leave it at that?

Also, since the IRS has stopped accepting determination letter application (except in limited circumstances not present in my case), is there a "failure" for submitted the PPA determination letter request late?

Any thoughts on this would be appreciated!