I am a little confused with creating the .fa adaptor sequence file.
I am using the NEBNext adaptor www.neb.com/nebecomm/ManualFiles/manualE7350.pdf

It says the adaptor sequence is
5 ́-/5Phos/GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT C/ideoxyU/A CAC TCT TTC CCT ACA CGA CGC TCT TCC GAT C*T-3 ́

do I add the sequence:
GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CUA CAC TCT TTC CCT ACA CGA CGC TCT TCC GAT C*T

Or is it the two sequences post digestion with USER enzyme?

According to the manual you've linked only the selfcomplementary part of the adapter would remain
attached to the fragments that enter the sequencing. Hence, you would only find this part of the
sequence in the raw sequencing reads and would have to filter it out. That said, usually all protocols
do not work at a 100% efficiency and it is conceivable that the final reads are contaminated with
partially and / or undigested vector sequence.

I would recommend to simply include all possible variations of the adapter sequence that could
theoretically occur and combine them in a fasta file and supply that as the input to the adapter
clipper module.

A short comment: Please don't use spaces and non-nucleotide characters (e.g. *) in the FASTA file

I hope this helps,
bes greetings,
Marc