What is the proper time to wait between lifts of foam if doing a 4" application?
The installer I used told me it is fine to wait a few seconds after a 2" lift, then spraying another 2". Only if doing more than 4" of thickness would you have to wait 6 hours between the 4" and 6" lifts.

Had a pretty strong rainfall over the weekend and the exposed roof (4" of 2lb foam between roof trusses) leaked like crazy.
I thought the foam would keep the water out pretty good. Keep in mind even though the roof has flat areas, there are a lot more sloped parts that also leaked.

The proper way to spray foam, is by a professional.

The roof wouldn't have leaked if the roofing had already been applied. Most all builders put the roofing on ASAP before any interior work like insulation, wiring, drywall, etc., are installed. Why didn't you? At this point, if the roof has leaked badly, you need to wait for who knows how long until all the moisture has dried from between the foam and the roof sheathing. I wouldn't add any more foam at all until the entire roof structure has thoroughly dried, and w/ 2 lb foam that could be a while. Is the roof even blacked in? In any case you might need to put a hold on everything and let the roof dry through the top side, which means not even putting down the roofing yet. If rain is a possibility before it's all dry and you can put the roofing on, you might want to have some tarps handy and cover the roof pronto whenever rain approaches.

We had to do the spray insulation prior to the roofing because of the design of the trusses. There wouldn't be enough place to work in had the roofing been installed prior to spraying. The rest of the house is all masonry so we don't have any moisture problems, it all dries up in a day or two without any negative side-effects. The foam installer came back and patched up spots we thought may have led to the leakage. Since then we haven't had any leaks. Biggest culprits were the double-joist areas that didn't get sealed before the rain hit so they allowed water to seep through.
The roof is now up and everything seems great.