Franklin Institute or Natural History Museum
China Town
SOUTH STREET AND EAT A CHEESE STEAK!!
Holts!
And for a squid like you...
Philadelphia Naval Shipyard along with
The USS OLYMPIA is permanently docked at Penn's Landing in Philadelphia, and is open for public viewing. It is the only American warship from the Spanish American War still in existence, and one of only four warships representative of the time period that exist worldwide.
is a must see.
As is the USS Constitution also at Penn's Landing.
http://www.ussconstitution.navy.mil/
Eat at Old Original Bookbinder's!
http://www.bookbinders.biz/events.php
Visit Independence Hall and walk a few yards to spend a moment in silence at Ben Franklin's Grave (right across the street from the U.S. Mint), be sure to place a Penny on it!
The Liberty Bell is right across the street. Betsy Ross's house is also nearby.
The Art Museum might be to your wife's taste and worth a visit.
The Toy Museum is also worth a visit if you have time.
Eat a Soft Pretzel with Mustard on it!
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That should give you a start, enjoy your visit!
*edit* And thats all very doable in 2 days except maybe the Franklin Institute, I can spend a few days in there easily.