1) Is a Ph.D. a near-guarantee of a spot in a skunkworks type of job (Microsoft Research and the like)?
No, as mentioned above. Only a small fraction of PhDs end up at top places, industrial or otherwise. A strong record of publications or impressive projects (and a good degree) is still no guarantee but is more important that the answer to "PhD: yes or no?" There is a big difference between a degree from a strong institution and from a lower-tier one as well. Also, the level of finishing students varies greatly. There are always some students, even at top programs, who end up getting a degree but if the work and thesis aren't strong, there is no chance of a good job at a research institution or lab.
2) Is a M.S. just as good for this?
No. Master's level programs are quite different than doctoral programs.
3) How does the 'letter of recommendation' requirement work if you haven't kept in touch with your professors?
A letter from a faculty member that says "I have no specific recollection of this student but my records show good grades" doesn't carry much weight. A strong letter from someone not in academia who is familiar with your recent work is probably more valuable.
One thing to be aware of is that in many programs, there can be a bias against older students. That is, supervising a doctoral student is a great deal of work for the advisor, and many advisors would prefer to spend that limited energy on a bright, promising 22-year old who may have an impact over a long period rather than someone who isn't as likely to have such a long career, particularly if they are likely to head to academia. Reasonable or not, this bias is present at many research institutions.
As mentioned in other comments, don't do it just for the possibility of improved job prospects. A PhD is difficult, and if you aren't doing something that you have a profound interest in and love for, you are likely to struggle.