You cannot edit out inconvenient sequences just because somebody or a computer program does not like the sequence. If your sequencing was good and generated a strong clean sequence then good science dictates that the result should either be defended or withdrawn but simply editing the sequence does not sound like good science unless you have repeated the sequencing and achieved a better result. If the sequences are not coding DNA sequences then stop codons are not relevant.

I think you can and It may be possible by looking at the three frames (+) and choosing the one which is longest. It can be done by ExPASy or by using Unipro Ugene free software and extract the longest ORF. If you could use a chromatogram to shift the frame, you can correct/adjust the length of your ORF and remove stop codons.