I did a set of cloak rules a while back, the basics were;
- ships declare they are cloaked (or uncloaked) at the start of the Movement Phase;
- cloaked ships are moved last, after all other ships and fighters;
- cloaked ships may not use any weapon, interceptors or Anti-Fighter, scout functions, or launch fighters. They may enter atmospheres and land on planets.
- While cloaked, the ship is treated as having Stealth 5+, and may not be fired upon from ranges exceeding 3".
You could also give scouts some anti-cloak capabilities, and allow e-mines to 'flash cube' (i.e. expose) them.