I'm sorry you're feeling so crappy (no pun intended).
Here are my suggestions:
1) Were you given any rectal meds? I believe those might be very helpful to you, like canasa suppositories or enemas.
2)Which probiotics and how much are you taking?
3) I would suggest you start a food journal, and see if a pattern develops.
4) But IMO, you might be amazed at how much diet is correlated, and at the very least if you find that SCD (specific carbohydrate diet) is too strenous, you should be dairy and wheat free. I think you may find it relieves some of your symptoms. You probably have certain food intolerances as well, which are a contributing factor. In my experience many doctors don't believe the diet/colon connection, but many folks on this forum can tell you otherwise (including myself).
5) Were you blood tested for vitamin d3 deficiency? How much Vit. d are you taking?
6) Alot of whey protein powders contain alot of junk and sugar in them. The only whey protein I can recommend to you is the one I use, which I know is the best on the market: Dr. Mercola's Pro-Optimal Whey Protein, it comes from grass-fed, no hormone cows, and already has digestive enzymes which makes it easy on the gut.
7) If the Lialda isn't working, you may want to go back to your GI and see if another med will work for you. But be aware that some of us are intolerant of the oral 5-asas.
8) If you don't feel you can talk to your GI, see if you can get a recommendation - perhaps through CCFA - of someone who will be more open to discussing treatment options with you, albeit most GI are not pro-LDN, so for that you'll still need to see your naturopath.
As far as LDN, if you're going to try the oral kind, I would recommend the hypo-allergenic formulation to prevent any reaction to fillers.
Otherwise, my personal preference is Ttransdermal LDN, as it bypasses the gut entirely, and gets absorbed by the blood stream.
Good luck with the naturopath - bring a list of questions for him/her.
And let me know if there's any way I can help you.