I've been expelled from the Temple my second time, is there any way I can get back in, and if not then what console command can I use without breaking anything? I haven't even finished my pilgrimage yet.

Two, I tried joining House Telvanni but they didn't like my other affiliations. I assume they disliked the fact I'm in the Thieve's Guild. What can I do to get around this, cheat or no cheat?

To join Telvanni: 1) your Intelligence and Willpower must be at least 30 and 2) not a member of House Redoran or Hlaalu.
Anything else shouldn't matter.

I hope being a part of the Sixth House (mod) will have nothing to do with it :/

PCClearExpelled "Temple" will get you back in.

Thanks. That just about clears up both my questions then.