USF started FB in 1996 as a I-AA independent. (I don't do FBS and FCS, they are I-A and I-AA as God intended .) USF became a I-A independent in 2001. USF moved to C-USA in 2003 and the BE in 2005. So that is four years as a I-A team, before moving to a BCS conference.
UCF started FB in 1979 as a D-III team. In 1982 they went to D-II. In 1990, UCF went to I-AA. In 1996, UCF became a I-A independent. In 2005, UCF joined C-USA.
So, if you want to compare USF's first four years, with UCF's first four years, then you are comparing USF 2001-2004 vs UCF 1996-1999.
This info on USF and UCF is not hard to find.
USF media guide - http://www.gousfbulls.com/ViewArticle.dbml?DB_OEM_ID=7700&KEY=&ATCLID=204909597&SPID=2981&SPSID=96971
UCF media guide - http://ucfathletics.cstv.com/sports/m-footbl/spec-rel/2010-media-guide.html
For FB records check out http://www.cfbdatawarehouse.com/
UCF BCS games 0-14
1996
Lost at 6-5 S. Carolina
Lost at 9-3 Ga Tech
1997
Lost at 8-3 Ole Miss
Lost at 5-6 S. Carolina
Lost at 12-0 Nebraska
Lost at 9-3 Auburn
Lost at 7-4 Miss St
1998
Lost at 8-4 Purdue
Lost at 3-8 Auburn
1999
Lost vs 7-4 Purdue
Lost at 9-3 Florida
Lost at 8-3 Ga Tech
Lost at 7-4 Georgia
Lost at 5-6 Auburn
USF BCS games 1-5
2001
Won at 6-5 Pitt
2002
Lost at 9-3 Arkansas
Lost at 10-2 Oklahoma
2003
Lost at 4-9 Alabama
2004
Lost at 6-5 S. Carolina
Lost vs 8-3 Pitt
If you want to extend this out to games over I-A opponents with a winning record, it gets worse for UCF.
From 1996-1999 UCF beat Toledo twice when Toledo had a winning record.
From 2001-2004 USF beat 8 teams with winning records, which includes the above Pitt win and a win vs #25 (ESPN) Bowling Green.
Currently, UCF is 3-45 all time vs BCS teams with none of them being against a BCS team with a winning record. USF is 29-36 vs BCS teams all time and includes wins against ranked BCS teams with winning records.
Since both teams went to I-A, USF has 22 wins over I-A teams with a winning record (at least one every year for 10 years) and UCF has 11 wins over I-A teams with a winning record (spread across 7 seasons in the 15 years UCF has been I-A).
BTW, the BCS stats do not include the 2 games each vs Louisville, Cincy and UConn before they also became BCS teams.