Say I have a Binayre Pirate with Cloaking Device, and at range 0-1 a Trandoshan Slaver with Cikatro Visago and Rigged Cargo Chute.

During the End Phase, can I use Cikatro's ability to swap the two upgrades?

The card for Cloaking Device says Small or Medium Base, and Rigged Cargo Chute says Medium or Large Base. Does Cikatro's ability allow you to ignore these restrictions?

No.

Restrictions cannot be ignored unless a card explicitly says to ignore them.