@psychobunny with regards to your suggestions on stripping out features, I'll have the devs take a look at the disabling options you pointed out.
Integrating with my application:
We have integrated to some degree using the SSO plugin and hopefully it will continue to be as problem free. We are integrating this with a custom Laravel application.
I am really not keen on using iFrames and would prefer a proper theme integration but if push comes to shove, I guess I'll have to settle for an iFrame integration.
At this stage, we're doing development in-house but of course if we run into issues I will shoot you guys an email. As for the theme design, I will definitely keep @trevor in mind. I have looked at his work and it does in fact looks very nice.
I really appreciate you taking the time to reply to me and give me your advice on where to start looking; it is very appreciated.