We were done exploring the tomb by 2pm and had plenty of time on our hands before our 6pm train. However, we were too tired to do anything and simply ate and napped in our hotel's cafe but if you have a couple of ours, do check out the Agra Fort..I regret missing out on it!
Here's a rough breakdown of my budget for two people for two days:
Hostel: 800 per person
We paid 1600 for a private room at Zostel. A bed in a shared dorm costs even lesser.
Train: 1500 per person
Gatimaan Express one way ticket costs around 750, you can opt for cheaper trains as well.
Food and Alcohol: 1200 per person
We easily survived on inexpensive local north Indian food, Chinese food and pasta from Zostel's own cafe, a quarter of Old Monk and a couple of beers.
Transportation: 1100 per person
Our full day cab for Sikandra and Fatehpur Sikri came down to INR 1800 i.e. 900 per person and we used local autos for sightseeing which didn't cost us much.
Rest was spent in buying tickets at the monuments.
I would suggest that you keep a separate budget of around 2-3k just for shopping because Agra's Sadar Bazaar sells excellent export quality leather boots and bags. The only catch is that the sizes are all mixed up and there are limited pieces available per size. You really need to have some time on your hands (and lots of patience) to dig out the best pieces. Other than boots, guys can find really great formal shoes and kolhapuri chappals too. All the vendors are quite open to bargaining so don't shy away from negotiating the prices.
Don't forget to get some of Agra's glorious Panchhi Petha for your friends and family as a yummy, edible souvenir. There are multiple outlets selling fun flavours like paan, mango, orange and even coconut petha.
Other than that, you'll find beautiful marble decorations, lamps, beaded clutches, anklets and boxes studded with semi-precious stones in Fatehpur Sikri.