a small problem occurs concerning the engrams I can no longer produce certain elements while they are researched

Try collapsing the structure and repositioning

I seem to have the same issue I have with Ultra Stacks:
Certian engrams (Mostly those made it a mortar and pestal it seems?) don't let me craft them even though I have learned the engram. I really don't understand this since I use the same 3 mods that Syntac uses. (Auto Engrams, Stack mod and S+)

Edit: Having mostly resolved the first issue, I'm now not able to pull items using S+ x.x

Try restarting the map (if I'm not mistaken, the dedicated S+ convert the resources to stack versions). It may even be necessary to collect the dedicated ones and put them back.

As for the craft, just collect and replace. This happens when changing your mod stack or when you start your world without a mod stack and after a while the mod is added.

Note that "converted" items in the stack version will have their widget different from vanila items