The Pi is supposedly going to have a camera that you can integrate later this year so you could use that natively. You might need to convert the sensor to infrared which shouldn't be too hard, just change a filter.
The GPIO should be able to help with your LED's too.
Thanks, Fireraisr, I had thought of using a flash with the stills camera to get colour, to supplement the monochrome IR videos, so there would be no need to modify the camera. Apparently, many animals and birds aren't too phased by flash, as it looks like lightning to them.
Although I have ordered a "B" for experimentation, (no delivery until mid-May ) this project might suit an "A" when they become available.
I have a holder for 4 AA 2900 mAH NiMH cells which will give me 5 volts for the power supply, and a cheap USB camera for prototyping. However at 700mA, the batteries will only last 4 hours, (ignoring the camera and lights) so i may have to double up on batteries to get a whole night's monitoring, or find a way to power down unused peripherals in software. Naturally the network and video circuits won't be needed during monitoring, but I don't know enough about the architecture yet to know how realistic it would be to put them into a low power mode.
1st Batch Model B (256M) running Raspbian, Pibrow case, with RaspiCam.
Model A (256M) running Raspbmc, caseless.