According to what I've read on these forums, the 3.2 is a noninterference engine, so you didn't screw anything up.
As far as the oil and muck, I'd go ahead and use the Gunk or whatever brand you want to clean it up and try to find a leak. The last time I had my junk disassembled to the point where yours is now, I went ahead and replaced the oil pump seal and front crankshaft seal just for the heck of it. They're cheap, and you'll not be happy if you have to take all that stuff off again later just to replace a couple of $5 seals.