Hi @sree,
I come from an age of merging and assembling reads using sanger data, specifically, using the electropherograms / trace files of many paired reads to merge like you are currently doing, as well as assembling a portion of a mitochontrial genome a couple of decades ago. Mainly using commercial tools like DNASTAR (Seqman), Sequencher, and Genious, etc.. I might have some insight... 
First, some of the above mentioned tools offer free trials that you may be able to use to merge your reads... 
However, I think there are some free and open source tools you can use to properly merge your reads which make use of the elechtropherogram files, basically similar to fastq in the sense that they have a quality measurements that can be used to guide the merging of the reads.
I've come across, merge_sanger_sequences, TraceTrack, and Tracy which may be able to help you merge your *.seq files from the sanger sequencer into a single sequence.
There are likely many other tools or packages in python or R that I am not aware of. But the key point is to use the proper tools to merge/assemble sanger reads rather than making up fake quality scores to merge your reads.
I hope this helps! 