I work as a G30 professor at Tsukuba.
Some of what is said her may be true for some G30 universities, but not all.
Last year at Tsukuba, about 50% of applicants were turned away. We take fewer applicants, but we take only solid applicants, and those we do take tend to do well (around 90-95% get scholarships - lazy people need not apply [not that they'll bother, hur hur hur]). As a national university, your tuition fees are not so important (which is why 1st year is free at Tsukuba [
http://www.global.tsukuba.ac.jp]).
Your GPA will be on the table, particularly in the first round of applications (paper based); however, in Tsukuba at least, a good interview (second round) can make up for a whole lot. We're also sympathetic of individuals who had difficult circumstances which are not of their making (family breakup, etc). Ultimately, if a course has 20 places, it's hard to justify giving it to the guy with the 2.9GPA over the guy with the 3.7, irrespective of interview performance (but not impossible).
Your military service is good, but it's non-academic, and will probably not be counted highly. Tsukuba is applying for GI Bill recognition currently (I know, because I'm heading it), so that should be a bonus, as all the G30 universities should be eligible (if they're willing to apply).
From what I know of APU, it provides a good education, strongly focused on Japanese language education. Maybe half your classes are Japanese language. It is, shall we say, rural. If that's good for you, great. It is not ranked highly, but ranking generally show research achievement, rather than reflect undergraduate teaching, which I gather is generally good.
Ultimately, you'll surely love wherever you go.
Apply, see what happens. Contact the universities, or their representatives - try and get a recommendation...
[edit; of course, I speak only for my own university, and I cannot speak for other universities, although their positions may be similar.]