So I'm using factorio extended plus with this and I would like to change the ingredients so that the overtiers use the highest tier of FE+ machine. For example the assembling machine overtier +1 would use FE's assembling machine 5 instead of assembling machine 3. But looking through the code, I cant seem to figure it out. I'm only doing this locally on my end. I don't mind not changing the sprites, just the ingredients.

To make your own private copy. First clone the assembling-machine-3.lua file, and add that name to data.lua. Then open {game install dir}\data\base\prototypes\entity\entities.lua to find "assembling-machine-3"; and open your favourite mod to find the entity prototype of your favourite machine. Compare the differences between the two "original" machines, then you can modify their respective line in the new file.
The most important changes are likely to be:
- machine name [line 7 of mod 0.18.0 assembling-machine-3.lua]
- crafting_speed [line 189]
- energy_usage [line 198]
- crafting_categories [line 188] - (Maybe some mods assigned additional categories.)

Module slots and ingredients are "automatically" handled by the code, from its original machine.

You have to do the above yourself, because I am not interested in providing overtiers of modded machines at all.
It is hard to keep track of ever-changing prototype definitions of vanilla machines (over experimental branch) already. It is not feasible to make a "smart" code to generate overtier machines from any sources automatically. As you can read from code, it actually takes non-trivial effort to set things right for EACH machine.
An important factor is that I do NOT play with FE+, Bob/Angel, or any other such mods. It would be a big pain for me to notice any changes (as I am not playing them) and to keep things updated. I have less-and-less time on Factorio modding already. Don't want to put myself in another time sink.