I'm falling apart

4 weeks in Peru, 2 left to go. I'll post more elaborately with narrated photos once we return home, but for now I'm struggling with a serious issue.
Prescribed doxycycline hyclate to prevent malaria, we determined we are to take this daily for the entirety of our 6 weeks here. I had no idea the side effects would be this harsh.
The first I was worried about is yeast complications, imbalance involving candida and potential gallbladder problems, and possibility (likeliness) of yeast infection in women. I have been taking a yeast balancing herbal supplement that has so far proven effective, but I now have one dose left, and no idea how to communicate this with a pharmacist.
Second: digestive issues. Any reader doesn't want to read this (sorry if you happen to be the rare one to come across this) but it's also more than possible to develop colitis from diarrhea as a side effect. This is the one cause of the intense abdominal pain and stomach stress I'm dealing with. I initially thought it was purely a gallbladder infection (if that's a proper term?) but all signs point toward.. Everything, more than I want to think about.
I honestly don't know why I'm still taking this antibiotic.
We're anticipating Macchu Picchu this next week, a 4-5 day trip involving bus rides, hiking along train tracks and staying in towns along the way.
This is the biggest of my excitement (!!) and of my worries. I know that I really have it in me to fix this, it's just a matter of changing my diet and getting medical advice. I plan to see a bilingual clinic tomorrow, I haven't been able to find assuring advice on travel forums I've been scouring.
About the diet, one thing every traveler has realized, and I'm certain of this, is that you aren't always in control of what your meal options are.
Having an apartment in Cusco is life saving. We try to cook as much as we can from the markets in town, where we can save money and obtain more - healthy fresh ingredients, beans, vegetables, regional fruits, fresh baked breads, suspect meats, fish, strange local delicacies. I've seen a lady with a bucket of frogs in water awaiting their fate to be skinned and boiled.
Though we've been lazy lately, I won't deny... Relying on our local super mercado for easy pasta and cartons of juice, sandwich ingredients.
This will all change when we get back into the ready and able mindsets of the unknown possibilities. I'm starting to miss hostel-hopping, utilizing whatever challenging kitchen available, finding our favorite sandwich place in town. This is what Lima, Yurimaguas and Iquitos were about entirely. Much more adventure. More on those experiences in future posts once I have access to a real computer (acquiring a new device when we're home...)
To conclude this scattered bit, I am hoping to find medications that will work along with the doxy without causing any other complications I'm convinced will lead to an ulcer - thankfully I'm aware of my hypochondria. I'm incredibly excited for the next week.5, we will finally be seeing the ruins of the sacred valley and putting our backpacks to good use.
Wish me luck falling asleep tonight.