Partial answer: Significant progress, not sure how to finish it off
The dots in between the squares...
These can be interpreted
There are also some other ways to extract similar arrangements of letters:
The data collected:
So what next?
Given the ASCII conversion I think the answer is:
Edit: I think my original answer was incorrect. I now think it is:
Lines 1 & 2: Developers encounter bugs often, sometimes bugs persist causing anger, especially in patches.
Line 3: No bug, no need for patching anything
Line 4: Developers often have to patch code
Line 5: ...
This is not a complete solution. I am going to drop some of my scratch here in case it inspires someone else.
On the subject of the cipher:
I have noticed that
Applying the decryption:
So, the answer to the question "Where is Lester?" is ...
As a bonus,
Okay I'm shooting my shot. I'm not good with ciphers or what not, and I could be on the totally wrong trail but...
Here me out here:
OP went clearly out of their way to introduce magic into this question, but after the first paragraph, magic is barely referenced. They are meeting at a university laboratory which is pretty ordinary, even the clue that was "...
I've solved the fifth hint, but it's a bit long for a comment:
One viable solution to the logic grid occurs if we guess that
The last comment above is wrong. There is only one solution. I leave it to you, @Annosz. :)
The six hint are highlighted in this image:
Fourth hint - solved by @Jens
Fifth hint: - solved by @Jens
The final solution and the logic grid is the following:
Edit: author says that my guess is wrong. Leaving it here for historical purposes.
My guess at the answer to part 1. Is it
All the symptoms check out, although I think the "irritated eyes, throat, sinuses" part is not so common. Though perhaps with such a long exposure...
I think this is how to place the pigs
Deusovi mentioned correctly in the comments that determining the final answer has to do with
Furthermore, as determined by Luke Bickell in the comments, applying the logic that
The grid reads
The answer is 11, I forgot to try linear combinations on the columns, I'm an idiot.
For example, the first element of the fifth row (a5,1 = 13) comes up as a result of the following operation:
a5,1 = (a1,1 + a2,1) - (a3,1 + a4,1)
So the answer is: (3+21) - (4+9) = 11