You are a little bit limited to what you can do with temp root. You can't load any custom ROMs or kernels with temp, you need s-off and custom recovery for that.
I think one the biggest things you can do with temp root is use root apps, such as wireless tether.

As far as removing apps, any apps you remove are going to be repopulated by the Stock ROM once you reboot. You can use Titanium Backup to freeze apps, this will completely disable them and remove them from your app drawer. Technically they are still there but not using up any resources. Frozen apps won't reappear after rebooting, they'll need to be "defrosted" before they are visible/active.

 

why cant stock apps be permanently deleted? just curious

 

I'm not sure of all the technical terms but basically once you reboot it does a check on system partition, once it fails it reflashes. I kind of like if you mess something up within a custom ROM, a reflash restores all the original settings.

 

One thing I noticed with titaanium when i froze sum apps then went to defrost it says i had like 3 defrost left or something so I jus gave up all together freezing apps and just not happily use the phone how it is with the temp root. I would like to have all the bs bloat and what not from bogging my phone down but idk i just take the good with the bad and hope the dev dudes come on with s off so i can join the leagues of many who are NOT forced to use their like "they" want us too.