Spending 2 Nights/3 Days in Prague

seems a good enough list of things to do but be aware many of the things in the Jewish may close early on the Friday best to check times.You can buy a ticket for entrance to all the main sights within the area.
Plenty of oppertunities for a show such as you wish. check this website.
http://www.bohemiaticket.cz/
you can down load tickets for many events or arrange to pick them up at the venue.last time I used them I got the tickets delivered to my hotel for a small fee.
http://livingprague.com/
this website has loads of good info and often has discount vouchers,
there is also a section on hostels and cheaper places to stay.
http://livingprague.com/hostel.htm
the guy that runs this website is a good friend of mine and his info is spot on.
This website is brilliant for working out what to see and do even has suggested intinaries.
http://www.prague.net/
your budget of $60 per person sounds reasonable but does that include your accommodation costs, if not it is plenty as long as you don't eat at high end places.Sill manageable if staying in low end accommodation but only just.

For the performances I would choose either at the National Theater. The National Theater is generally a little more devoid of tourists in tennis shoes. The Two Widows is an interesting story and poignant since you will be in the Czech Republic. If you want to sit with Czechs buy the best seats. For an evening with tourists purchase the cheapest (the music will sound the same).

Now, since you have a similar question in the Budapest forum, let me suggest that you are doing an awful lot in a little time.

Thanks tremendously for your comments--I hope to follow up on all your suggestions and finalize plans very soon.

Thanks for the advice--absolutely loved Prague! So very glad I had three days there. I did not see a performance, or the Slav Epic which is closed at the moment, but accomplished so much more than I had planned it was definitely a highlight of my time in Europe. I will be traveling back to Europe next year, and would welcome any advice on other places in the region that might make for as memorable of a trip (if possible). Thanks Again!

Sincerely,
David

Interesting that the St Virus Cathedral isn't on your list. We stayed at the Green Garland http://www.uzv.cz/about/
In old town near the clock, walk across the Charles Bridge up the hill to the Cathedral.