Hi, @spartanscroller Terry,
I haven't downloaded or made this pattern but, it just appears to me that
you always want some of the dowel rods to stay attached and you want some of
the holes to be larger so you can remove that tray from the other dowel rods
without sticking.
The pattern should have had a better description of the dowel rods but, I would
just cut the ones that go into a 1" tray less than 1/2" long dowel and the dowel that
goes into the 1/4" thick bottoms, make the dowel rod abt 1/4" but, they are only inserted
into the hole abt 1/8".
I hope you got it figured out and show us your completed project.
God Bless! Spirithorse