Hi All,
I'm back from Iran and I thought I'd fill you in on some of my experiences in case you're planning a similar trip in the near future. Thanks to everyone who provided leads and great advice.
in terms of programs:
if you're a male and interested in studying farsi dehkhoda institute is the way to go. it's in tehran, class is five hours a day, and it's a real program with real teachers. the cost is competitive, but be advised that they do not provide housing for women.

i did a 4 week farsi intensive at the university of esfahan, $800 including a studio apartment. the staff and administration at the university were incredibly frustrating and often bordered on incompetant, the teachers rotated on a daily basis, but esfahan is second only to tehran in its attractions and social possiblilities. i would recommend asking for a private instructor and doing a six-week program there. you have to be really motivated to make this program work for you.

i also did a four week program at the women's hawza in qom, jamiah al-zahra, it was cheap (around $200) and included room, board, and excursions. it was an amazing experience learning and living in Qom. IEB (the islamic education board) sets up a ton of speakers and high profile events (we heard khatami speak at a juma in tehran, met with khomeini's daugher, and a half dozen ayatollah's including ay. ameeni). there's also excursions to numerous cities including hamadan, esfahan, tehran, and mashad, the academic program during the summer is for international students from all over the world and is conducted in english, but besides the tafsir class the standard of education was disappointing for someone coming from a rigorously critical western university setting. the women's program is significantly different from the men's. our lecture units were: hijab in islam, feminism v. islam, spousal selection, ethics, and tafsir. it was a lot of "feel good about islam" and doing dawa type stuff that i wasn't really into. get ready to pray at least five times a day and visit the haram constantly.

thanks to the blissfully affordable public transportation system (volvo and mercedes buses) i basically traveled to almost every major city, but the highlights for me were esfahan, rasht and massuleh to the north, yazd and of course, tehran. i limited my solo travelling and didn't have many problems; like pakistan the man on the street situation can be really irritating, but it was just that-irritating i didn't really feel like i was in danger.
the lonely planet guide was definitely helpful, hit and miss in some cases, but it's the closest thing to the yellow pages you'll find.

anyway, overall it was an amazing and eye-opening trip, my farsi got better, and i feel like i came away with with a lot.
drop me an email if you have any questions about trip planning or programs, i'd be happy to give my input.
happy travels and thanks for the great advice!