So I have it set that lings, zealots, and a couple other units have some upgrades but not others. Hydras and lings both have run speed upgraded but not attack range/attack speed respectively, and zealots do not have leg enhancements.... however I have those upgrades researched for zerglings and zealots as default to make it harder to kill them when the CPU owns them. The problem I'm having is it seems sometimes the upgrades are researched by default when you start as those countries...

What happens I'm thinking is the units are pre-placed for the computer and thus have the upgrade... but when you mind control / randomize the country that you want and you get control of those units with the upgrades researched already so it doesn't require you to research it... How can I change this?
I have an idea but I want to see if there's a better way (my idea is to remove the existing units when you "get" that country and then recreated them at the location that already exists to create them in the first place.

When you give units from one player to another, then all the inheritable upgrades are transferred, so you can preplace the units for an unused player with no upgrades (P9+ is fine) at the beginning of the game then give those units to computer and players later.

oh ok, will my method work as well?

Yes, if you remove the units that have the upgrade and place units that do not have the upgrade, the resulting units will not have the upgrade and will thereby not transfer the upgrade from a mind control/give. (I think that's what your idea was saying.)

it is exactly, thanks a lot =D