Welcome to DTT Stacy, Looks like you scored a sweet little machine.
I will tell you now. Reinstall the stock mufflers and the airboxes w filters. If you cant clean up the stock filters to "acceptable". Guys, have removed the old paper and replaced it w uni-filter foam. OR find a good pair on ebay or cmsnl.com
After you make your seat mod and so on. Get her running properly. Enjoy her this summer. After doing your homework about the filter and pipe modifications.
Then make the decision. Through education you will find it takes some pretty extensive work to make her run correctly w the changes your currently planning to make to the aspiration.
If you insist on having a bike that runs crappy, when it does run at all...(fouling plugs due to rich condition, between the speeds of 30-60mph. due to the new Uni-filters and shorty exhuast mufflers.
Atleast keep and store the stock mufflers and filter/boxes. That way once your sick and tired of walking/pushing. You will have them ready to re-install and she will run good again. The summer after this one.
I offer all the manuals you guys will need for free download. Notice I dont offer the crappy Clymer manual.
http://www.hondabrat.com/2013/04/manuals.html
I also have made more extensive posts discussing the POD and PIPE mods your looking at.
http://www.dotheton.com/forum/index.php?topic=63133.0
http://www.dotheton.com/forum/index.php?topic=60728.0
So good luck, most importantly be safe and have fun.