Hi Margaret - I also see a naturopath and TCMP (Traditional Chinese Medicine Practitioner). I have to admit I haven't had the issue with lack of periods, but I did have issues with adrenal glands, which can definitely wreak havoc on your fertility. I was also prescribed vitex by my naturopath (who is a doctor; not all of them are, so be careful) but you have to be well informed about how to take it - some docs suggest only taking vitex on days 1-14. It didn't make enough difference for me so she started me on a specific Adrenal Support supplement that really helped - eventually I was able to taper off to just rhodiola. I'm NOT recommending that you do any of this (don't go picking up random vits 
) so only take what your naturopath or OB/GYN prescribes and you're comfortable with. I also do acupuncture, but with my TCMP, who specializes in fertility acupuncture, as some acupuncturists can actually do damage in days 14-28.
It is interesting that your OB prescribed clomid if you have a thin lining. It affects everyone differently. Regardless, I'd question her on it.
For 'naturally' starting a period, one thing I know has worked for some people is parsley. Parsley can cause uterine contractions and cause menstruation, in the right circumstances (your situation sounds complicated). You can buy a bunch from the produce section and chop it up and put a large quantity in your meal or boil it into a tea to drink throughout the day. Even if it doesn't work, at least you'll have fresh breath 
Feel free to PM me if you wanna talk 'natural' - some people confuse this with following old wives tales (like pineapple core) or witch doctors so I try not to bring up my non-western medical experience here, since it's not really the purpose of the board.
Best of luck!