Hi Sarah. It's sounds awful the problems you've had with the PEG but it sounds more like the hospital stay, the illnesses and the general trauma that have caused the feeding issues and even if it were removed things basically won't change, it's just time needed for everything to settle and slowly start to improve. Can I also say that an ng tube is much more uncomfortable than a gastrostomy in the long term. You have just been very unlucky.
If you have been advise overnight feeding is safe then I would do so but not 500 mls to start with. 200 very slowly and build from there. Elevate the head of the cot on blocks (probably already do!). Overnight feeding is not unsafe unless they are big wrigglers, but we used to put the tubing down elli's pyjama leg and the pump at the bottom of the bed.
Something that a lot of people don't realise that the less food you take in the less hungry you feel. Anorexics feel little hunger whereas obese people, despite huge food intakes are usually constantly hungry. So ensuring plenty of food even if it is via a tube so that the child is well fed and putting on weight, will stimulate appetite not depress it. Obviously feed orally first, but I gather that the formula or bottles going down the tube are what's prompting the vomiting? Vomiting is a major cause or oral aversion as is refluxing. Also trying to feed a reluctant child ends in aversion.
It sounds as though your DS may still be having some intolerance to the formula or to dairy.
You are unfortunately in the same situation we were when el was 3.5. Vomiting continuously on formula, poor weight gain, constipation, tired, still eAting little 
. I personally think these formula feeds are the work of the devil 
although they do suit some children. However they are full of rubbish and lacking in so much and seem to be the cause of a lot more gastric problems than they solve, like reflux, slow emptying and most of all vomiting. Let's face it a feed that the body is rejecting on a regular basis is something not good for it!
What turned the corner for us was feeding blended diet. Which is just good quality food, blended, sieved and syringed down the tube. A mum from here put us onto it and we have never looked back, as have a few hundred parents who are on a Facebook site, blended diet UK. All with stories just like yours and ours! 2 years on el is normal height and near normal weight, no constipation, healthy, very little vomiting, on no medication and never needing a fundo OP. Still very orally averse, but he has cp which affects speech and mouth movements although he has a safe swallow. He can and does eat things though and we have many instances of children being weaned off their tubes after being given blended diet.
It's probably too soon for you to go that route at the moment as it's all very new, but do bear it in mind for the future. Meanwhile go back to dairy free, and try a small overnight feed to build m up for eating. Also look at the different medications suggested.
Hope all this essay helps
Xx