As you, we were also advised not to go near the Townships even with a guide, and on the other hand we were told that it was something that had to be done. We wanted to do it and knew in our hearts all would be ok if we chose the right tour operator.
The following tour company was recommend by our apartment owner:
www.townshipcrawling.com
(click on History of the Townships and at the bottom of the page is a link to Thuthuka Tours)
Sorry can't remember the tour guides name but he owns and runs the tours and his wife owns a Shebeen where you can request a traditional South African meal. We rang him up and said what we wanted from the tour and he arranged it all including a meal at his wifes restaurant - it lasted approx. 5 hours. He picked us up from our apartment and took us to all six townships and showed us new and old living quarters, a school, a witch doctor/healer, shops, craft stalls etc. etc. We also visited a Township B&B (Vicky's B&B which my Husband and son want to do next time - I'm not too sure, as I like my comfort). She is well known and you can do a search on the internet.
This tour was by far the best experience of our holiday and I would highly recommend people go and see how the majority of South Africans have to live. It was a mix of emotions too.
We hired a car from here (UK) through Holiday Autos for our 3 week trip inbetween flights - all ran smoothly.
Not sure where the best places are to shop in Cape Town - maybe someone else can help you there, as we did most of our shopping in Durban. I just remember The V & A Waterfront Mall was very, very expensive.
We didn't take Travellers Cheques as again through forums we were told it was a better deal to use cash machines (switch card) and credit cards - we also took cash (Rand).
Hope I've answered all your questions and welcome anymore you may have.
Regards
Holly
p.s. Another good website I used was:
www.fodors.com
(click talk, then Africa & Middle East)
www.bbc.co.uk/holiday
(do a search on: You Call the Shots - South Africa, and there is a wealth of information)