Part of the problem could be the refreezing of the ice cream. You know when you take out ice cream, eat at it for 5 or 10 minutes and then put it back in the freezer...and then the next time you take it out, some of the ice cream is a little icy and bit grainy?
I'm not sure you can solve this if you use the same recipe. Instead, I would recommend using the highest fat chocolate milk you can find instead of using melted chocolate ice cream.
I really doubt the pudding didn't get dissolved completely. If that really was the case, you could heat the mixture before you put it in the pie crust.
A very common type of pudding is a pudding made from liquid thickened with starch. It is usually made with milk, but you can use other liquids as you see fit. Fruit juice will probably work best. For starch, use plain potato, corn or wheat starch. The "absolutely no fat" condition is very detrimental to the taste. A trick to make it taste richer would be to include some whey powder. Any sweetener will work - sugar, baking sweeteners like honey or agave syrup, or artificial sweeteners (keep in mind the max temp for artificials). You can enhance the flavor wit the usual suspects - vanila, cinnamon and other spices - and/or serve with syrup poured over. Adding food coloring is also a good option, as it affects the perceived taste too.
To prepare the pudding, use a base ratio of 1 part starch to 10 parts liquid (you can change that later, depending on your preference for firmness). Mix the dry ingredients (sugar, cinnamon) with the starch in a small bowl. Stir in some cold liquid, around 1 tbsp per 25g starch, until you have a slurry. Bring the remaining liquid to a boil. Remove from the heat and quickly stir in the slurry. Return to the (reduced) heat and let simmer for some minutes, stirring contantly. Stir in the liquid ingredients (e. g. honey, molten caramel). Pour into the form(s) and leave it to cool, at best overnight. It will set and should be firm enough to slice. Alternatively, it can be eaten warm (and still soft) from bowls.
You mention Jello. I don't consider gelatine jellies to be a "pudding", but maybe this is a language problem on my part. You can make a gelatine "pudding" with powdered gelatine, just follow the instructions on the package. Gelatine itself is pure protein and does not contain fat.
It is also possible to use modern thickening agents to thicken a juice or another liquid to a more or less pudding-like consistency, but this is unusual in home cooking. If you are interested, look up guar gum or xanthan gum. There is a free e-book oh hydrocolloids often linked here on SA, but it probably goes much beyond what you need. Still, you can search for it if interested.
Best Answer
Unless the package instructions are very different, yes that should be fine. A typical pudding mix will consist of
the main ingredient, required to thicken the liquid (typically milk)
especially for the "instant" types, others let you add sugar separately
sometimes "the real deal" like vanilla, often artificial.
like chocolate shavings or caramel crumbs for an interesting mouth-feel
not really neccessary, IMHO.
(A very basic pudding mix would be corn starch and cocoa powder, btw.)
So if you combine mixes, you combine starch with two (or more) different flavourings, which will be absolutely fine. Just read the labels to make sure you are adding the correct amount of milk etc.