if you're still there... can I ask how long he's been off gluten/wheat? I'm worried you may be falling into the same trap we did, by being persuaded to cut out/ reduce gluten before the right time - I know it seems very sensible and like the best thing when you see the difference in your child. But it has caused us, and will cause us many extra problems, and much MORE pain in the long run.
If it has been months, then do as you plan. If it has been days/weeks - get him back on gluten NOW! check out the CUK website, but I think it is 4 portions of wheat a day - eg weetabix, slice of bread etc. A toddlers bowel can recover very quickly, making diagnosis difficult. He will need to be on gluten (as above) for 6 weeks/ (now changing to 3 months) before both the anti-body (blood) test and the biopsy to avoid false negatives IMPORTANT.
Apparently the biopsy isn't very uncomfortable at all, and having it done now, rather than in four years time (like my daughter) will avoid the pain (and embarrassment) resulting from reintroducing gluten after the coeliac body has ceased to produce 'gluten' anti-bodies - the reactions to gluten often get dramatically worse once this has happened.
It sounds like your son has a big problem with wheat/gluten, so it needs to be cut out of his diet ASAP. BUT if it is coeliacs this will be for the rest of his life and he will benefit hugely from knowing his diagnosis for certain. Think reluctant-to-help health professionals and teachers etc, rebellious teenager, laid-back student.
Sorry if this sounds overly dramatic - I just hate to see people following 'common-sense' advice like I did and then paying the price later. BTW, as a nursery nurse I have seen quite a few pale 'road-map' tummies, but all the other symptoms you describe sound very suspect - does he have any behavioural/ emotional issues as well?