I have my original 2.0 matching number engine ready for storage while I run another engine in my car. Can folks give me some guidance on how to prepare an engine for long term storage?

The usual method people do is to take it all apart and put all the unlabeled pieces in boxes.

Optionally, leaving it outside and oncovered is the other method.

Another option is Mystery Oil poured
down the intakes and WD-40 on
all the linkages...
Keep a wrench handy and turn it over
and move the linkages every time
you walk by it..
Been 45 years and this still turns easily
and the linkages still move..
Click to view attachment

45 years? Time to put it into a 914!

It will never go back into the car in my lifetime.
The car hasn't been driven since the mid 80's anyway.
From 1975 till then it had a 2.5 SS in it.
That engine started out as a 1965 911 engine and became
too valuable not to sell.

The next owner will make the decision to keep this engine stored
or put it back in.

I have started the process of building a 2.0 with S P/C's and Solex cams.
Just got to keep pushing my mechanic to get it moving along.

Spray marvell mystery oil on the cylinders, little down the intake, shrink wrap and put it in the corner of your basement. On a pallet or something to keep it off the floor. Turn over by hand every 3-6 months. Or have it rebuilt and put it in your livingroom.

My 3.2 is in the downstairs livingroom with 4 motorcycles...