Pizza Fox

I think everything that is required to be submitted will be evaluated. But your University GPA (which probably contains the majority, if not all, of your upper level courses) will certainly be more relevant, thus it makes sense to assume that the committee will put a higher weight on it. Also, your old GPA isn't bad at all, and the committees will also consider trends in GPA, especially the improvement since junior college. Finally, it's worth noting that although many schools will ask for an overall, cumulative GPA from each school, many programs will identify several "key courses" and give a larger weight grades to these courses. For example, many programs in my field will care the most about certain physics classes and upper level astronomy classes.

You include the transcript. Some of my credits were done at a community college and I absolutely was required to include those. In fact, my degree granting institution just listed it as generic "x credits at Y college" on the official transcript (I was given a copy that I opened upon graduating) so those grades may well be essential.

In most application forms I filled out, the Education section asked for details on all institutions attended and transcripts from these. (Sometimes, they will only ask for institutions from which you received a degree, instead of "all" but the majority asked for "all"). So, this will be the correct place to enter details from your junior college and it is likely you will need to request a transcript from them too. 
During my Masters, there was a course I took that was officially listed at another neighbouring school (but taught jointly by faculty at my school and the other school). Through the Ontario Visiting Grad Student program though, students from my school were able to take this other course for credit. But because I did that, I needed transcripts from the other school as well when I applied to PhD programs! The credit appeared on my "home" school's transcript, but it just says "Transferred Credit" or something like that, no course details. So the other school's transcript was required to show what the course was and what the letter grade was.
If you are worried about this, most schools should have their PhD applications open by now. You can log in to / create accounts for all these schools and see what requirements they are asking. If you need official transcripts, make sure you are easily able to access your old school's transcript request service. In my case, the "transfer" school decided that they will only take transcript requests that are snail-mailed on legal sized paper, which added an extra couple of weeks in the processing, so I was glad I had plenty of time to sort it out

Here is some possibly bad advice from someone who was once in a boat a little like yours and has just gotten accepted to a couple of very cool interdisciplinary programs where you can do stuff a bit like what you are saying.  But the road between A and B is not necessarily easy.
 
The first thing is: don't try to reinvent the wheel (this is a bit what your post sounds like).  Everyone already knows about Foucault, you can use him to think about institutions, the formation of subjects, blah blah blah.  Do not think of yourself as a "Fouauldian" or an exegete or else you will not get where you are trying to go.  Take a step back and ask, "Why I am interested in MF in the first place? What questions lead me to want to think about MF?"  Basically you need to decenter Foucault from your idea of what your intellectual project is if you want to do something other than disciplinary work (if you want to go into English lit, for example, it might be fine to be that into Foucault - but then you are just an epigone)
 
My suggestion is to plan to spend some time away from the academy for a couple years supporting yourself in other ways and reading as many books as possible.  You still have an enormous amount to learn and all it takes is time (you don't need a professor to tell you, just go read all the stuff you know you haven't read).  You may find that during this time, and in the bubble-bursting experience of no longer being in a formal educational environment, your idea of what you are interested in will change and become more refined.
 
I spent two years outside the academy, and I'm now finishing up an MA in English which I found deeply unsatisfying but which helped me understand what it is that I DO want to do.  It's only now, four years after my BA, that I'm really even qualified to begin doing the kind of interdisciplinary work that you seem to want to do.  And it's now finally paying off, but only after a period of four years which was not especially emotionally easy.
 
I would take some time off, find yourself a bit and read for several hours every day, apply to a disciplinary PhD program in English or Philosophy (make sure you get funding), and then bail with the MA and apply to an interdisciplinary program.  Some good candidates might be UC Santa Cruz History of Consciousness, U Minnesota Discourse and Society, , Berkeley Rhetoric.  You could also apply to these programs right out of BA but probably much harder to get into.
 
basically, don't be in a hurry.  you can't do what you are saying you want to do if you are in a hurry.
 
good luck