Long story short my valve springs got mixed up on my 400m. There are 2 different lengths of spring one taller, one shorter, on which valve does each of them go?

 

From the rockauto.com site, it would appear that they are as follows:
Longer spring = intake; shorter spring = exhaust.

Some years show the same height spring for either valve - assuming yours is a 78 or 79, the above should be accurate.

While you're at it, you might want to double-check the free height of your springs - if they're much less than the height shown at RA (I'm thinking 0.050"), you should install new ones.

 

From the Ford Bible: int/exh
Free length - 2.06"/1.93"
Installed height - 1.8125" -1.844"/1.6875" - 1.7187"
Solid height (coil bind) - 1.33"/1.20"
Out of square - 0.078" (5/64")

Specs are for both 351M and 400

Don't forget that the rotators go on the exhaust valves. (I know you're aware of that, but I had to say it).