I doubt anyone knows where the source is now. Interplay of course owns the rights, but I suspect they haven't made an effort to preserve it.

I only vaguely recall the resource placement. I think you can ignore the "normal" numbers. Originally the entire map was going to have low levels of resources, and that's what the "normal" values refer to. The concentrate numbers are all that remain. The "low-high" values are a simple random range. Seperation is the rough distance, in squares, between deposits. Diffusion is a measure of how many squares a deposit occupies.

I don't recall how infiltrator experience worked.

Alien experience was based on kills, I believe. And no, it wasn't random. Rather, it used a mechanism similar to the unit upgrades. That's as much as I recall.

We had pretty much no documentation for file formats, ever. Like many projects, we simply added code to read / write sections of the file as we went. Since no other application needed to know how to write those file formats, there was no formal doc.