I-m an american backpacking through Europe for a total of 88 days at the moment but would like to remain flexible if I decide to stay in another location for a few more days.
All of the countries I am visiting are in the Schengen Zone except:
Ireland (4 days)
UK (7 days)
Do these count toward the 90 day limit or will I be able to add 13 more days no problem?
If you have a multiple-entry tourist visa for the Schengen territory, you can hop in and out as often as you please, as long as your total number of days in Schengen does not exceed 90 in a 180-days period. Does this answer your question?
Your stay in Ireland and the UK does not count towards your days in Schengen.
So if it is 88 days in Schengen + 13 days in the UK and Ireland you'll be ok.
BTW, you'd get more detailed answers if you posted your travel details:
Plan to enter Schengen at Paris airport, flying in from ... on Jan/Feb/ XXth 2010. Will then travel to ... and to ....
I'll fly back home on the ...
You get the drift.