Hi @sree,
Did you try merging the reads using the tools I suggested in this post? From later posts in that thread it appeared that you did this. If so, there is no need to merge forward and reverse reads with Ns. In fact, joining with Ns is likely incorrect. A properly constructed capillary sequencing experiment should generate overlapping reads, that you can merge/assemble given the tools I referenced. There should be no need to join with Ns, as you've already merged them.
In fact, I reverse complimented the sequence in the PCR_14_ITS_4_F02.fastq file and was able to generally and manually align it to the PCR_14_ITS_1_F02.fastq:
It's not great, but I assume these reads are from two different isolates, with slight sequence variation (or errors?). So, the alignment is not perfect. Anyway, these look highly overlapping.
Again, once you have these merged reads you can follow the OTU tutorial I linked. Can you provide me with the forward and reverse reads for a couple of isolates?