My question is if I built a level 2 building can I in the same build order build the new unit that became available? My first thought would be no since at the beginning of the build order the building didn't exist but if I have the workers and resources I didn't see anything in the rules that said I couldn't?

You have to stick to the following sequence while executing any Build order:

- workers & transports (*)

- units (*)

- upgrade building

- build new module

- build new base

Steps with (*) require also having a base on the active planet.

Because you can't upgrade any building until you finish purchasing new units, unlocked ones must be build when you execute your next Build.