I hope you're coming for at least 3 months, 'cos you'll need it ;-)
Inverurie would make a good base as it has a good range of restaurants with a top Indian (Planet Spice) and has enough of everything to keep you supplied. You can also get a train/bus to Aberdeen which could be handy for your better half whilst you're out stone hunting.
Having said that, if you went self-catering, there are some excellent farms selling their own produce (We get 90% of our food from The Store at Foveran) and it's some of the best grub we've ever had. They even do their own ready meals, hand made on the farm with their own ingredients which are also gorgeous.
There's a range of museums, galleries etc. in Aberdeen and you should both put aside an hour (it won't take much more) for the Marischal Museum which has some interesting prehistoric finds from the area + loads of other esoteric stuff. Once you've finished there, wander down the hill to 'Books n Beans' for a guilt free snacking experience and a huge second hand bookshop.
Aberdeen is a cultured enough place (in the right areas like any other city) check out the Music Hall and His Majesty's Theatre along with the Lemon Tree and you're sure to find something to occupy the evenings.
Having said that, September has very long warm evenings if you're lucky, and you could always be enjoying the last rays of sunshine at Easter Aquhorthies around 8-9 at night. :-)
You're coming at the right time though, as 90% of the crops will be cut & you should be able to access the circles with ease. Have fun :-)
