The crux of this problem, as given in Hint 2, is a Vigenère cipher. To apply a Vigenère cipher, we need three things: the alphabet, the ciphertext, and the key.
The easiest to figure out is the alphabet. The note tells us that
The base range isn't the standard, but it's still standard.
We also know, from the extra information, that the alphabet likely ...
Gradual Deduction :-
Step $1$ :-
Step $2$ :-
Step $3$ :-
Step $4$ :-
Step $5$ :-
So I have solved this already, the rest remaining is to find the name of the physicist and the message he left behind, well I am not finding any clue to the nonogram though.
Given that the solutions to the cryptic clues are as follows...
...we next notice that these answers can be split into three groups...
Next, we should notice the numbers in the corner of each box that contains a clue:
Finally, as pointed out by @HTM in comments (nice spot), let's focus on the cells containing the 'holes', and specifically...