Ok great, thank you. Based on your description of Charlie's signs, it sounds most like large intestinal diarrhea (colitis), although it could have a small intestinal component to it as well. Large intestinal diarrhea is typically associated with increased urgency and small volumes more frequently.
Given the chronic duration of Charlie's GI problems, I don't think that intestinal biopsies are a bad recommendation, however I do think there are other routes you could pursue prior to surgical biopsies (especially since you are hesitant about the surgery).
First, abdominal ultrasound is a great imaging modality for evaluating the intestinal tract. They can evaluate wall thickness (which can become enlarged in cases of inflammatory bowel disease) as well as wall layering (which can become disrupted in cases of cancer). They can also look at local lymph nodes as well as liver, kidneys, etc. If Charlie hasn't had an abdominal ultrasound, that would be my first recommendation.
Additionally, since Charlie has had signs since he was a puppy, I want to make sure that intestinal parasites have been completely ruled out? There can be some tricky and unusual parasites that require special testing to rule out.
It's great that your vet tested for EPI, since German Shepherds are the poster child for that disease and Charlie's signs seem to fit well. Another consideration would be a gastrointestinal panel (for example there is one at Texas A&M) that evaluates Vitamin B12 levels and folate, as these are things that can be supplemented. This is a blood test that can be sent out by your veterinarian.
Overall I think that Charlie could benefit from visiting an Internal Medicine specialist (if he hasn't already). Internists are the diarrhea experts and they would be very thorough in evaluating Charlie and making recommendations.
Lastly, regarding the surgery - I don't think you need to be afraid of it necessarily, although surgery always carries some risk of complication. We perform intestinal biopsies routinely and the dogs typically do quite well afterward. That being said, if you are uncomfortable with the idea of surgery, then I recommend pursuing other options for diagnostics first.