1.a) Use "in"
1.b) "all of the items"
- It is already after the delivery date
- The delivery date has already passed.
2.b) "Estimated" (your estimate was made in the past so it was estimated)
- Please excuse the delay
- We would like to apologise for the delay.
I can let you know what I would write if you can answer a couple of things:
- what do you mean by simultaneously, exactly? Are you waiting for everything to become available before delivery?
Here's a rough idea:
Dear customer (use their name here if you have it)
Unfortunately, we don't have some of the items you have ordered in stock at the moment.
We realise that it is already after the estimated delivery date and would like to apologise for the delay. We will notify you as soon as the items become available.