Great stuff and unbelievable job of taking care of your health! Thats how I got into health and holistic medicine was the clearing of my skin through natural methods.
I haven't heard of milk thistle causing Acne before. However it seems to be exactly what you said with your body not being able to detoxify and eliminate the new load of toxins coming out of your liver your skin has to jump in and "save them" or you rather or you'd get very sick. Acne in most cases is actually really a good sign even though it sucks it means the body is getting that crap out of you instead of succumbing to the toxic overload.
Anyways I would do exactly what you said. Get some colonics if you can afford them and do a kidney cleanse. Then I would do a few Liver Flushes at least 6 and see how your skin is doing. Also definately afford trouble foods that can cause inflammation to help heal that leaky gut and make sure your getting enough fermented vegetables/probiotics. Fermented Veggies are the BEST Acne FIGHTING FOOD IVE EVER FOUND. It is because they assist in so many of the bodies functions related to acne development.
On your skin...I guess proactiv worked for you but it never worked for me. I actually wash my face with clay. Leave it on to dry for like 30 min and take a shower. Afterwards I put on a formula I made based in aloe mixed with lavender tea tree and neem oils. I also put hydrogen peroxide on newly popped pimples because it dissenfects and helps heal the wound faster.
Hope this might help. If you need anymore feel free to Personal Message me. Good luck and let me know how it goes! I hated acne and want to help anyone that is frustrated by it!