Have they checked you for Celiac Disease?  It could cause all the symptoms you are mentioning, including lactose intolerance. Many doctors still don't think to look for it if the patient is not having diarrhea, but the fact is that many celiac patients never have any gastrointestinal problems at all.  Celiac disease can be ruled out with a simple blood test nowadays.

As for non-dairy alternatives, here are my favorites (my family and I have tried just about every brand of every product on the market):

• Blue Diamond Almond Breeze, Original Flavor (almond milk with no added sweeteners). Similar in taste/texture to lowfat milk. Everyone in my family loves it, kids & hubbie included.  Can use in any recipe that calls for dairy milk, though puddings will turn out a little less firm.
• Hemp milk, unsweetened, any brand. Creamier than almond milk.  Can use in any recipe that calls for dairy milk.
• SoDelicious yogurt, Plain (yogurt made from coconut milk, w/no added sweeteners).
• Tofutti brand cream cheese and sour cream.  I've tried all the brands out there and these taste the most like the real thing.  Follow Your Heart brand is not bad either.  Some of the other brands are extremely unpleasant.
• Cheese - Daiya brand has the most loyal following.  I personally find all the commercial non-dairy cheeses to be gross, but home-made ones are truly delicious and melt just like real cheese.  You need a good blender to make them.  Generally they contain tree nuts, which are full of healthy fat, but they can be made lowfat (to be honest though, it doesn't sound like you need to stick to lowfat unless that's essential for the SIBO). Feel free to PM me if you want some tried-and-true recipes.
• Homemade soy yoghurt.  This is high in protein, unlike yoghurts made from other nondairy milks.  All it takes is a quart of unsweetened soy milk and a little box of yoghurt starter from any health food store. You can find recipes online.  Unfortunately the only unsweetened yoghurt on the market was made by WholeSoy and they have gone out of business.  There are great-tasting sweetened soy yoghurts on the market if you are able to digest that much sugar (I can't).
• Nondairy creamers - Blue Diamond makes an almond milk creamer; SoDelicious makes a coconut milk creamer; and Silk and I think Pearl makes a soy milk creamer.  I think there are some unsweetened versions.  My favorites are the Pearl & Silk.
• To substitute the fat, calories, & protein you were getting from cheese, consider raw unsalted nuts & seeds.  My favorites are pistachios, cashews, pecans, walnuts, almonds, brazil nuts, & sunflower seeds.  Eating a handful or two a day has been shown to have many health benefits (as long as they are raw, i.e. not roasted; and not salted).  Brazil nuts seem to go bad faster than others so I keep them in the freezer.  Some people love chia seeds.  Pumpkin seeds are great too but I think they pretty much have to be roasted.

Good luck to you!  I hope you feel better soon!

I am 12+ years out from my gastric bypass and I have ALL kinds of digestive issues, including lactose intolerance. Do not eat cheese and yogurt as they are full of lactose and will kill your gut. Take a good quality probiotic (see consumer reports here). And don't use whey protein if you are still using those. I use two non whey protein powders. One is a vegan protein powder. The other is beef collagen (I am a pescatarian but I make an exception for collagen as it helps my joints). The links that I embedded will take you to my reviews of those products that I published on my website. 

Do not eat low fat. Sugar not fat is the culprit in obesity. Many of the Key Opinion Leaders, doctors who are experts in diet, are telling us to eat many healthy fats like fresh water fish, walnuts, avocados, etc. I just posted under the diet and nutrition section my comments about Dr. Lustig's New York Times best seller Fat Chance: Beating the Odds against Sugar, Processed Food, Obesity and Disease. You may read my post here.

Good luck to you!