Sounds like your body is going through quite a time with die-off at the moment, that first couple of weeks whilst your body is desperate for Sugar but not getting any makes you feel rough as hell. To me yours makes sense then, it's desperately trying to get rid of all the toxins (hence all the aches and pains) and all your normal organs are trying to perform their duties but your system is having a bit of an overload. So your systems is stressed, you are probably stressed (I was massively)and I expect the yellow is just a sign of general unease in the stomach.
I've been on the anti-candida diet for 6 months and hopefully right at the end of it now, I've been following a really strict diet (similar to you but no yog...so yes just meat, fish, veg and general herbs and spices...the odd grain here and there to keep energy levels up). I also take about 3 different anti-fungals, vitamins, probiotics etc. Die-off took a very long time with me and I kept making the odd mistake (unintentionally) and as you can see from this forum, different things react to different people- i can't take any nuts for example but I took ages to pin this down.. I've got to the stage where I KNOW I'm right at the end of this thing and just being meticulous about every sign and symptom to knock it on the head once and for all. I still have days of real die-off symptoms although it's much less severe now.
I think a green stool is as you say, connected to your veg intake..nothing unusual about it as far as I know. Healthy liver function....avocado, hot water with a slice of lemon in the mornings, broccoli, brown rice, eggs, carrots, garlic, spinach,asparagus, avocado.. Vitamin C as well ...and they're just good all round to be honest.
Sounds like you're doing all the right things but it does take a while and more patience than i could ever have dreamt of having. This forum is great though- if only to help you realise there are other people out there suffering the same thing and you're not totally abnormal!