The number level of a security clearance has nothing to do with the number of years they look into your background. The levels go like this:
Level 1 - what we used to call "Confidential" is now the lowest clearance (they will ensure your references are real people)*
Level 2 - what we used to call "Secret" requires a more detailed background check (they will actually talke to your references)*
Level 3 - what we used to call "Top Secret" requires the most detailed background check (they will talk to your references, ask them who else you knew and then talk to them)*
"ER" is "Enhanced Reliability," the lowest form of security check and is not considered a "clearance" (essentially ensures you are who you say you are)* Not sure why you were told that this requires a more extensive background check than Level 1.
*NB I'm being somewhat facetious here. There actually is more to it then this.
All of these things take time and if you've lived outside the country during any period that they need to look into, things will be delayed. Even if you've never lived outside Canada, things can be delayed for any variety of reasons (e.g. if there's another person with a similar name that has been naughty).
Security clearances are determined by occupation and sometimes by specific position, not rank. As Alea said, a logistics officer will normally have a lower clearance (i.e. probably Level 2), while a communications research corporal will have a minimum Level 3.
On another note, do NOT accept enrollment in one occupation with the firm belief that you will be able to transfer later. It is never that simple. In fact, it can be a very difficult thing to do. Finally, if you have your heart set on being an LCIS Tech, the closest naval occupation would be Naval Electronics Technician (NET - Communications, Tactical or Acoustic - initially three separate occupations that converge at a higher rank level). A Naval Weapons Technician (NWT) works with weapons systems. In simple terms, the NET works on the guidance systems (computers, radars, etc), while the NWT works on the gun itself. One job is much cleaner than the other, but both require a fairly high level of training /education. The NWT training is concentrated more on ballistics, physics, etc than on electronics.