I am unable to handcraft Engine unit. I've tried a bunch of different things to try to make it work and I am unsuccessful.
perhaps am I doing something wrong?

I was able to download the 1.0.0 version and edit the info.json
and change "factorio_version" : "1.1",
with this modification, I can handcraft Engine unit

That is strange.
Are you playing with other mods?

yes I am playing with other mods
I will try it with no other mods.

Try enabling/checking the "All characters" setting of this mod.

ok so I've identified that
Bob's Character classes mod (https://mods.factorio.com/mod/bobclasses) is causing a problem.
But the only way it will craft the Engine unit is if I already have an Iron gear wheel already crafted it won't automatically queue it up.

I just tried it with only Bob's Character classes and Hand Craft Everything and it works. Probably another mod is causing this. Check what mods modify the Iron gear wheel recipe.

Though I see that I have the effects of "All characters" reversed :(

oh that was it "All characters" reversed
turning off "All characters" fixed it
but I'm still having the does not queue up prerequisite items problem

Version 2.1.3 fixes the inverted effects of "All characters"