with all your issues we need to start sort; get the basics working first and move forward with the others.
you need to start with:
A) Get physical links working (green LED)
B) Get a subnet manager going and make sure logical links are also working (amber LED)
C) upgrade all components firmwares to the latest possible (switches and HCAs)
once those done, then move to other thiings (protocols, ibping, vmware, your app, etc)