This is a real mess, and in a number of yet unidentified areas that makes it too long and detailed to resolve here. As you probably already now, these issues compound over time with each month that goes by making many of the separate issues ever tougher to resolve.
In the big picture, priority #1 is to make sure that no accounts have been or are about to be escheated to the state, after which it may be difficult to reclaim the funds. This would also involve withholding being paid to the IRS for the account of the TIN of record. If the custodian knows of a death, they freeze the account from further transactions with the exception being to send the proceeds to the state. If these accounts have been frozen, there have been no distributions so the balance would only change due to investment results, which have been very good for the last 5 years, so I don’t know why you think that the balance declined.
Otherwise, the only way to unravel this is in chronological order, year by year because each fact about the accounts triggers a different required action. I would try to get organized and make a list of date and forms you have. You provided mom’s date of death, but what about dad? List each account, name of custodian and owner of account and the year of that documentation.
For each account, you need to determine the exact beneficiaries at the date of death. If individuals, those accounts do not fall under the estate executor’s responsibility. The last thing I would worry about here is RMDs, it is more important just to work with each custodian and identify which documentation needs to be provided for each beneficiary, and of course the death certificate. Again, the accounts are probably frozen meaning that no distributions should have been taken, and that is why there are no 1099R forms. If no distributions have been issued, there will be no need to amend any tax returns. 
This adverse situation could be made impossible without an experienced and cooperate IRA custodian for each account. Given the situation and age, the custodians are probably preparing to send the accounts to the state if they haven’t already. The beneficiaries need to prevent that if possible by cooperating however they can, with the custodians and with each other.
This situation is way beyond the purpose of this forum. Best I can offer is to address specific questions you have. There is no way I can provide an entire game plan or this post could become the longest on record here.

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