Need to fix .sqn genome annotation file prior to uploading to NCBI

Question

[kristina.mahan]

I made a .sqn file using tbl2asn from my genome .fsa and .tbl files. I uploaded to NCBI and there are errors that need to be fixed:

FATAL: 1 feature contains '()'
FATAL: 3 features contains 'flavo'. Possible parsing error.  Has the product name been truncated?
FATAL: 3 features contains 'phospho'. Possible parsing error.  Has the product name been truncated?
FATAL: 1 feature contain 'lipo'. Possible parsing error.  Has the product name been truncated?
FATAL: 2 features start with ','
FATAL: 3 features start with '-'
FATAL: 1 feature contain 'glyco'. Possible parsing error.  Has the product name been truncated?
FATAL: 6 features start with ':'
FATAL: 1 feature contains '='
FATAL: 2 features start with 'and'

1. Do I fix these errors in the .sqn file or in the other files and remake the .sqn files?
2. How do I fix these errors in the .sqn file? For example: FATAL 1 is NAD() synthase in Contig_110. So does that mean I need to manually change NAD() to NAD+ in the .sqn file? If so- is it just using a unix tool for find and replace?