There are a number of books and websites (including shailot ve'tshuvot of recognized halachic authorities) on the topic of Halachot for Soldiers. I would strongly recommend anyone in this situation consult with your local Rabbi or posek. Below is a list of a few of the sources I know of:
Pants: Rabbi Adin Shteinzaltz (Even-Yisrael) has written that there may be situations where pants are more modest than skirts, observing that Jewish Yemenite women traditionally wore skirts on top of pants. What I've heard is the general recommendation against pants are because they tend to be more form-fitting than skirts. I know religious women who have been told, in various occupational settings, that loose pants are acceptable; again, talk to your rabbi. (Yes there are some who claim they are entirely prohibited as "men's clothing", but that seems to be less the case today.)
Israeli hechsherim: see this question, describing some of the differences between "more-preferred" and "less-preferred" hechsherim. Many years ago, Rav Goren was visiting the Gruss Kollel and he was asked about the basic kashrut level of rabbanut with regards to terumot uma'asrot. He said (back then) that all were recommended, except for Rabbanut Haifa, which was using a controversial loophole suggested by a young Rav Shlomo Zalman Auerbach. I could also say that chicken & turkey tend to have less kashrut complications than beef, and that anything that says "gelatin" on the ingredients could be more complicated. Keep in mind that Hazal left certain leniencies for soldiers, so basic kosher may be good enough for you. Please make sure you're eating enough to stay healthy and do your job.
Shabbat: training is a complicated question; many things if done in a strange way (such as dialing a telephone with the knuckle of your thumb) become less prohibited, if this works for your situation. As for anything operational, if your commanding officer says it's of vital importance, I heard Rabbi Herschel Welcher in Queens say that an army can't work if soldiers are constantly questioning their orders. I also heard a story from Rav Benny Lau about a soldier who had to write on shabbat, he wanted to write only the things he thought were important. Rav Shlomo Zalman Auerbach told him, al tachshov, tichtov. "Don't think, just write."