Him eating only waffles, french fries, and crackers is entirely your fault...sorry. Why in the world are you serving him these things?
When their appetites are delicate, such as at this age, you ought to be making every bite count. You couldn't be going more wrong than waffles and french fries!! I know they're easy, but so are a lot of healthy options...and the thing is, he won't starve himself. If you ONLY SERVE healthy food, he'll eventually catch on that if he wants to eat, here are his options.
Just finished reading your post, btw. My youngest has celiac disease, as well as a dairy intolerance, so I understand what it's like to be creative and I STILL don't feed my child this way. Just because something is "gluten free" doesn't make it a health food...nor does organic...etc. And just a note...if your child doesn't NEED GF food, you shouldn't be giving it to him in place of the regular things he could have (for instance, real whole wheat bread.) GF food is often high in sodium. Wheat germ really isn't a good thing to feed a child, either...just being honest.
Even if he screams for a day...or two...he'll get over it. I PROMISE you he won't starve. Try fresh fruits. Peanut butter offers good protein...make him a peanut butter/whole wheat/banana sandwich. Sweet potatoes or homemade sweet potato fries...baked...instead of french fries. And there's really nothing wrong with potatoes in moderation...just not fried. Try adding yummy additions to mashed potatoes...we like broccoli in ours.
I'm sorry if I came off a bit harsh at first, btw, I just don't want to go back and erase. I understand picky eaters...my first one was that way...but I eventually just said "enough is enough" and only offered healthy options.