A lot of the upgrades are missing in 1.12.2 version

They are not "missing". They have been removed for various reasons. The port from 1.10 to 1.12 was pretty hard, and it is almost a miracle the thing we thew together works.
Modmuss50 took over the mod and is maintaining the 1.12 version. Use this instead:

https://minecraft.curseforge.com/projects/engineers-workshop-reborn