applying for change of status to temp visa while applying for perm resid... problem??

Hi, I am here on an R-1 visa which has a limitation of stay: "the workers total period of stay may not exceed five years." Is stay defined as physical presence, so can I deduct any time in the past 5 years when I was not in the USA? Or is it just a straight 5 years from my initial date of entry under R-1 status?

Also, I have a new job lined up, still religious work, just different employer. I want to submit a I-129 to change my status (that is change employer) - the current wait time on this is 2 months which would be quicker than applying for an Employment Authorization (EAD) along with applying for permanent residency (my spouse is US Citizen). Would applying for change of status to temp work visa (R-1) raise any flags if I apply for permanent residency at the same time?? it's not like I'm applying for a new R-1 or even an extension...just a change of employer.

Any EDUCATED help would be greatly appreciated.