Hi,
the multiple envelopes is actually a bug. If you combined phone and envelope and got another envelope from the unversity afterwards, you should uncombine phone & envelope first (just click on the item in the inventory and then select the option) and not get another envelope from the university once you combined them again because this state could break things going further. You should either have one envelope and one phone seperate or 1 item with them combined, not the combined item and an additional envelope or phone in your inventory.
Regarding the university puzzle, it's all about getting into the office of Polizeikommisar Glocke, there's an item under the bridge that helps with the priest (also check out the hint from steam) and you also should take a look at the phone settings, maybe this will give you a push in the right direction on how to solve it.
Best regards Christian