I know there must be a better way to cut the notches
please explain how you are cutting the notches now.
I remember as a kid, we had a large parakeet cage and
my mother would takes sticks off of an orange tree and
cut the slots with a regular carpenters hand saw.
when I had chickens, I used my hand held Skil circular saw
to cut slots in larger branches and bamboo for roosting sticks.
if you have a hand saw, pull saw, etc and a vice or something
to hold it steady, you can do it.
if you want to drill holes to accept other dowels, one dowel must be
larger to accept the hole - if they are the same diameter, you must
do the half-lap technique (as mentioned above).
you may be overthinking this a little.
[what do you do with that laundry list of tools you have access to?]