Any suggestion on how to go about doing this?
Well, you've got a lot of code that's not broken up into subroutines, so it makes it a lot less readable and maintainable, e.g. harder to figure out exactly what you're doing. I assume that you're looking to see how well it performs. If so, you can use Devel::DProf. Or, if you have two ways of doing something, you can compare them using Benchmark.

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... but I'm having lots of trouble with parsing.
What kind of trouble? Is it slow? Giving errors? Taking up too much resources? Unexpected results?

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There are so many parameters to set up. Any suggstions on which ones I need to accomplish my goal.

A few things:

• Is your code working? Seems to me like you're using all your variables. In terms of whether you need to go through all those steps, I don't know... this is definitely a case where breaking it up into subroutines could not just encapsulate your variables to a given subroutine, but help to let you know whether you really need it. I assume you've read the docs on cpan, like Bio::Seq?

• Your definitions

  my @k = keys %$monomer_ref;
  my @v = values %$monomer_ref;
  [download]

  
  are redundant... if you use keys %$monomer_ref; or values %$monomer_ref instead, it would be one less thing to set up.

• I'd suggest using Config::Std, or any of the other modules out there that lets you set configuration parameters in an initialization file. You could also use GetOpt::Long, if you like to set things from the command line.

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The current code I'm using gives me 1000's of OUT files. There has to be a better way than having to read get of the OUT files.
Well, is there a reason you have to use so many files in the first place? I've found Log::Std to be very useful for logging information.