Jana, I think you need to see your primary doctor and/or a gastroenterologist. Food shouldn't come out in the same condition it went in.
Yeah, I'm gonna have to see a doc. Will go with my GP, first. It takes AGES to see a gastro around here -- they are soooooo busy doing colonoscopies.
I understand the GI tract pretty well, since I had achlorhydria (no stomach acid) for years before it got diagnosed. I had increased infections, reactive hypoglycemia from undigested food "dumping" into my small intestines, etc. That lead to my B12 deficiency and then, finally, figuring out what caused it all.
Annie, I thought about your lack of stomach acid WHILE I was throwing up. I think mine's ok -- no other symptoms. BUT, I am slightly anemic, now -- found that at my last GP appointment. I took iron for a couple of days -- made my stomach worse (apparently this is common). Now I'm eating every iron rich food I can find.
Peristalsis is how food moves through the GI tract. Gastroparesis is when the stomach doesn't empty food right away. Both can be affected by MG. But I suspect that's not the only problem.
Undigested food on "the other end" means that you aren't digesting your food on the front end. It doesn't have to do with how fast it moves through the GI tract but how it's being digested. It usually happens when you don't have enough stomach acid. You can have hypochlorydria (not enough stomach acid) or achlorhydria (ay-klor-high-dree-ah). You may be lacking in certain enzymes too, which is even more complex.
My food appears to be digested "in the toilet". (Can't believe I'm being this discriptive!) It only looks undigested when I vomit.
Achlorhydria is compounded by food sitting in the GI tract, undigested, and putrefying. All of this can lead to leaky gut, infections, inflammation and more autoimmune problems.
I could drone on and on about this topic, so I'll stop there.
Do you feel bloated after eating a meal? Do you ever feel hungry within a half an hour to an hour and a half after eating? Does food move through quickly or slowly (from start to finish). It would help to keep a journal of how you feel from when you eat to, well, when it's flushed.
Nope, I don't feel bloated.....but, Topamax killed my appetite so I don't eat very much. I feel hungry at meal times, more or less. I have noticed that it can take a couple of days before food I eat "comes out". (The iron pills made my movements very dark -- and it was a couple of days after the first pill before I noticed the color change.) Apparently, my entire GI tract is "lazy". 
Other things that significantly affect how food moves through are being hydrated enough and having enough fiber.
I have been constipated ALL of my life -- until Mestinon. I am the QUEEN of fiber -- I search for fiber-rich foods. I also hydrate more than anyone I know -- in excess of 80 oz per day.
What I found most interesting when I researched this back in 1999 was that you need acetylcholine to make stomach acid (and gastrin and histamine). I found an entry in an old encyclopedia that listed something called "Myasthenia Gastrica." I guess no one pays attention to it anymore because it's not really talked about.
"Myasthenia Gasītrica: weakness and loss of tone in the muscular coats of the stomach; atony of the stomach."
Whatever is going on is not normal. Do you need an expensive and invasive upper endoscopy to figure it all out? Not necessarily! What did our ancestors do before electricity and machinery?
Maybe do some research and then talk to your primary doctor.
I read about the endoscopy -- and sort of FREAKED. With my swallowing issues (you are usually awake) and the dangers of anesthesia in MG.............I agree -- having this all in my head BEFORE I see a doc is THE way to go!!
What I take to digest my food - which I don't recommend taking until you have that talk - is Betaine HCL. It's a mild acid, usually made from sugar beets. When people hear "acid" they often think of battery acid or other very dangerous things.
If you don't have acid or not enough of it, this is not a dangerous thing to take but a very good and useful thing. If you find out you have this, we can always go on ad infinitum about it later.
Annie
And I'm so worn out that I didn't even bring up pancreatitis. If you have that, it's serious. My dog Teddy had it. I highly suggest seeing a doctor right away. What Teddy had to do was have pancreatic enzymes on his food and have a high fiber/low fat diet. Again, you have to figure what's going on first. There could be more than one thing.
I know -- pancreatitis crossed my mind. My dad died from pancreatic cancer, so it is always "lurking" in my brain.
Thanks SOOOO much, Annie. I feel better just "talking" about it. Waking up in the middle of the night with stomach aches........so distressing. I don't have this problem all the time -- it seems to go in cycles. I had even thought about Crohns.
I've upped my Mesty the past couple of days -- after reading that it is sometimes used for Gastroparesis. I do think I'm a little better.