Keith have you ever done an align bore and hone job? I have and facing the thrust surface is part of it, but used caps can pose a problem if they are off as not enough material to remove. Same problem with mis registration at the parting lines as everything come out of the caps. You don't want to be getting into the block side.
Machine shop can be a hard business to make money and not everyone wants to fix someone else's mess. The blame here is the shop that lost the caps and they should have made things right. In this case you need to find caps that are close or use new ones, otherwise your wasting a lot of time and risking screwing up the block.
You might have read the first response to his query. Charles Machine just completed the work on my new FE block. It states that the block was offset bored, align bored and square decked. Yes, I am VERY familiar with the process. There are TWO different thrust bearing widths on the FE.
I doubt the material would have been an issue. It doesn't take two months to assess the suitability and condition of five main caps for the job. I rarely find any production shop/rebuilder that knows anything about the FE. I have had the same issue here in NE Texas since I relocated from So Ca. There are a couple of great head people but I have only found one machinist who really knows his way around blocks and has all the machinery in house to get them done. Few are worth their salt when it comes to early Fords, especially the FE.
I absolutely find fault with a shop that SITS on a job for two months then tells you they can't get it done. Both jobs I had done were assessed before the block was left with the machine shop. There is no culpability on their part for a previous shop's incompetence.
Charles Machine took in the job I just had done on 28 May and it was done on 04 June.
We have some great builders/machinist that participate on this forum.
They are generally informative, helpful and very capable. The poster is within driving distance, so I recommended someone here who I have had do work that was competent, timely and fair. This is the second time this gentleman has tried to use a local shop and was screwed around and waited a ridiculous amount of time for a job which prompted him to pull his parts and take them elsewhere.