Congratulations on your marathon! I will run my 4th in April. I do not have the issues you have had with weight loss and digestion problems, and have always had regular periods even during peak training times. However, some women have amenorrhea, I believe, from having too little body fat. So, it may be that even if you are now putting weight back on, you still don't have the body fat. Muscle is heavier than fat, so you may be weighing more, but still not have enough boy fat to menstruate.
I discussed my running with my RE, and he said that running is not a problem with conceiving or even with pregnancy unless you are getting into really high weekly mileages, like 50+ miles per week.
You may want to get your body fat tested, and also see your doctor to find out what's going on.
hope that helps