Call and I arrive!
First and foremost, Rufio knows what's going on with regards to the recruitment side of things better than I do.
1. It really is a HUGE toss up right now as to your chances. It sounds like you are still in the Navy Reserve right now, have you thought about becoming a CEC LDO? Other than that option, I will say that it fluctuates as to what the boards are willing to overlook or be a non starter for them. When I applied back in 2013 I didn't have my PE but I work in the construction industry. When I started meeting people I found that there was a little bit of everything, some had PEs coming in some didn't. Some like myself work in a comparable industry, others didn't. Heck, I know one guy that was working as a pharmacist but had his engineering degree! So it really comes down to the board's composition and what those individuals are looking for in applicants. However, you really, REALLY don't know unless you try. I will say that your experience as a Bee is definitely helpful as is the fact that you already have an MS. In your job, would it be possible to get enough experience under a PE to sit the PE exam? It is starting to become a hard limit for promotion to O4.
2. This is definitely when people try to take leave. Try Rufio's suggestion regarding NRD Philly.
3. Not going to lie, most CCs I have experienced on the RC side aren't really well instructed in officer programs and so forth. There are likely some that could offer advice and help you get the documents you need from the Navy side of stuff but they can't help with the actual submission.
I'm sending a PM your way.