1
I think it’s pretty complicated for a beginning HST workout. There are a lot of different exercise to find RMs for and alternate between. Not impossible, but a lot of extra overhead work to keep track of. Also, the standard and IMO best way for hypertrophy is to make the last 2 weeks negatives (assuming you can do them). Negatives will contribute a huge amount to hypertrophy.
2
Yes 12 exercises is going to start to get long once into the 5s and things get heavy. Full Body workouts are better made up of compound exercises. If you are going to use isolation exercises they should be for a specific reason, like you can’t get it done with compounds (Calf Raises), or to bring up a weak point (Overhead Triceps Extensions) to specifically target the long head of the Triceps.
3
The cycle is actually 9 weeks if you include a 1 week SD. Changing things is really a matter of personal preference. I wouldn’t change anything that is working. However, it doesn’t hurt to change things to find out what works best for you since every person is different. I find it’s best to stick with a set of core compound exercises that I’ve found work Deadlift, Squat, Chin Ups, Press, Dips, Row, Shrug and Bench Press. Throw in Calf Raises and Lateral Raises and you can hit every body part.
I suggest you read the Simplify and Win thread.
http://thinkmuscle.com/forum/showthread.php?16246-Simplify-and-Win!
I think you will get much more out of HST, or any training program, by learning about how to use it and tailoring it to your needs rather than following someone else’s template.