New, need advice on my plan

[1991NSX]

Hi,
I am 36, out of shape. I am 6' and (finally got up to my wanted weight) of 182-185lbs. I got a Bowflex from my friend (an older model). I want to gain flexibility (I work behind a desk) and am very stiff, even my legs now. I've been working out now since the beginning of Nov. However, I was getting acclimated and just in the past 3-4 weeks with research I've finally changed my routine to the following. side note: (I have a very fast metabolism - never have to worry about being over weight.)
I cannot do most excersises due to either my shoulder/elbow or arm, popping, grinding or clicking. I refuse to do them because I don't want to aggrivate the problem so it does it more in my everyday life. (Rows and butterflys are out)So in hopes to gain flexibility and strength and to get tone and add some definition and ultimately some muscle here is what I have changed and came up with. Any ideas to help me get to these goals would be appreciated:

I am now eating a breakfast (where I never did)and am taking a multi vitamin. I also take Whey supplement after my workouts with my bowflex. I know free weights are better, but due to room for now I have this to work with:
Wed/Sat: 4 sets of 12 - curls
4 sets of 12 - bench presses on the 45 degree incline (I never feel any strain in my chest - just arms/shoulders doing this???)
3 sets of 10-12 skull crushers(?) for tricepts - just added these, tricepts are hard on my arms so I have to be careful.
I do lots of stretching and using an excercise ball in between sets and reps....


Sun/Tues/Thurs:
3 sets of sit ups with weights(holding the handles by my collar bone) to work the abs and lower back
3 sets of 12-15 squats
2 sets of 6-8 dips (hands on a chair behind and my feet on the exercise ball)
2 sets of 15 situps and a few other ab excersises for strength.

I only do stretches on Monday's and Friday as I rest. A little different from most, but due to my equipment and my physical holdbacks due to the tendons or muscles popping/clicking will that routine help me build some muscle? I will add to the reps when I get to 12 or 13, then add weight. I've been doing this for about 3 weeks, before that I was lifting half the weight as i didn't know what I was doing before tweaking (reading stuff on here) and getting acclimated.
Thanks!
Jim