Video is new enough in the DSLR world (only 1 or 2 generations with video so far) that you will have problems finding good used deals on DSLR's with video. I honestly don't think you would be able to find any in decent shape under $400.
For full manual controls (separate wheel controls for aperture and shutter speed) you need something like the Canon 20D or 30D (both can be found under $400; the 30D only slightly, the 20D usually $300 or less). You can go older and get cheaper (10D, D30, D60) but I would not recommend it, as the 10D and older bodies are limited in their lens choices. On the Nikon side, D70, D80, D90 models all have dual control wheels as well. I am not sure on the pricing on used Nikons, but surely at least the D70 would be within $400 or close to it.
For time-lapse stuff, on the Canon side you will need a separate control module (not sure about Nikon, but I think the same applies). It plugs into the shutter release socket and sends signals to take photos every so often (basically it is a programmable timer that triggers the shutter). It can also take long exposures (in bulb mode - more than 30 seconds). The Canon model is TC-80N3 and it is about $170. I have one, and it is fantastic. There are generic equivalents to be found on eBay and elsewhere for much lower prices. Note, Canon has 2 kinds of shutter-release sockets: one found on the pro/prosumer bodies (3 pins in a little round socket) and one found on the consumer Rebel line (looks like an audio mini-jack). The TC-80N3 works on the pro/prosumer bodies (those being the Canon bodies with one or two digits: 1D, 5D, 7D, 20D, 40D, etc.). So be sure to get the right one for your kind of body. Again, I recommend that you go with a 20D or 30D which will use the 3-pin type of connector.
For under $400 with body and lens you are pretty much looking at kit lenses. These are usually 18-55mm lenses with variable f/3.5-5.6 apertures. If you can, try to find the Canon version with Image Stabilization (IS), usually called the 18-55 IS. But it is not likely you will find one with a 20D or 30D body. If you get a 20D body without a lens, you can probably find an 18-55 IS for around $100. The older, non-IS versions go for less -- $50 or so (although it's a bit hard to tell since they're rarely sold on their own).