If 400A is what you need to operate a multi-family it is reasonable.
Most all new homes take a 200A for SINGLE family. Mine is
THREE/MULTI-FAMILY.

I think this will be the easiest way to accomplish my goal:

1. Upgrade #1 to 400A
2. When I want to run #2 and / or #3 off the 400A panel I will shut off
the utility (won't be on anyway if there is no tenant) and remove the
SE cable from the panel.
3. I should then be able to wire it in such a manner to make it a
subpanel of #1. I know code does not require a main breaker, but I
could leave it in there I do believe. My feeder cable will come from
the 400A panel and be wired to a 100A breaker.

This will require some work since I cannot leave an unused wire in
place when I am not using it.
The only big question. When I rewire floors #2 and #3 I will be
running ONE CABLE from the basement to subpanels on the 2nd and 3rd
floors. When I go to single-family it will mean my two main panels (#2
and #3) become subpanels of #1. This means I will have TWO SUBPANELS
in that configuration and I do not know if that will meet code.

Frank