UWA is notorious for slow responses to e-mail...when it is working. Many on here have stated that it is best to contact them by phone.
http://www.ugandawildlife.org/index.php?option=com_contact&view=contact&id=1&Itemid=104
Last time I went I had to wait three weeks for an e-mail response. If you still can't get them by phone, do a search on this thread to look for travel agents in Uganda that can get you the permit. I think they charge $50 US to do this. Don't go on their gorilla tours though - too expensive!
Going to the National Parks independently is pretty easy. In Kampala, go to the bus/matutu station and tell one of the guys in the white coats where you wnat to go. They will take you to the right bus/matutu. People on the bus are pretty helpful too if you have to get off the bus before it's final destination. When I went to Kibale NP, I took a bus to Fort Portal and then a matutu to the NP. They dropped me off right at the gate. Same with Mgahinga NP....bus to Kisoro and then scooter to the National Park. You'll save a bundle doing it yourself over goign through the travel agencies. The UWA homepage gives info on how to get to each of the national parks.