I'm very much a rookie at FX loops, in fact I just ran my first EQ pedal through my Mesa Triple Rec this past weekend, and it sounds amazing.

Do I have to use heavy duty guitar speaker cable to do this? or can I just use a standard 1/4" guitar cable? I am currently using two 10' heavy duty guitar speaker cables, could I just replace them with two 2' standard guitar cables? what are the pros and cons?

Also the only pedals I use are a Boss Chromatic tuner, a Morley Power Wah and Digitech Whammy, should I be running any of these through my FX loop as well? If so why? what are the pro's to doing it this way?

Standard cable. Speaker cable aren't shielded and you may get noise. None of the pedals you listed should be in the loop normally (except the EQ), but you can always experiment.
generally speaking,
any guitar cables are fine, i use a standard 1/4" cable. since it's between the pre-amp and the poweramp, the signal isn't too powerful. the speaker cable is probably degrading your tone a bit...

also, as a general rule of thumb: distortion, boost, and wah go in front of the amp, and modulation goes in the loop. it's up to your ears, but most would agree it works better that way. keep the whammy in the loop, so rather than bending your original guitar signal, it bends the recto sound. the EQ can go in front or in the loop; i prefer the loop to fine-tune the amp signal, but someone else might prefer to mess around with the dry guitar signal.

hope this helps!