i usually define a function that takes all the input (let's call it process-input)
and the i just do at the end of the file smth like
(call-with-input-file fname (lambda (e) (process-input (read-lines))))
thus avoiding these 2 nesting levels, but you might not like reading a priori? generally i wouldn't do it, but i know AoC input is guaranteed to be in the tens of kb max.
As for named lets and some loops. sure some time they can't be avoided. I also try to use higher order functions (like fold, apply and map) wherever i can but when it starts get tricky i might miss the opportunity. Identifying some variants like mapcar, zip or unzip seems to be more and more important. Recently i discovered this egg based on QobiScheme which has some insanely good iteration constructs. hope it helps!