Since the field expanded to 16 teams in 1986.

I could only find the seeds listed for 2004-2016. Is there a site that lists the seeds for every year going back to 1986? CollegeFootballDataWarehouse that no longer exists might have had that info.

Could mostly figure out 1986-2003 by looking up the teams for that year or trying to find info on the NC game. For example, teams winning the NC game with 3 losses (1990 GSU, 1991 YSU, 1992 Marshall, 1998 UMass, 2002 WKU, or getting their 4th loss in the NC game (1993 Marshall) obviously weren't top #1 vs #2 seeds. Couple other were #1 vs #3s like 1994 #1 YSU beating #3 Boise, and 2000 #3 GSU beating #1 MT.

But as far as #1 vs #2 in 31 NC games with field of 16 or more teams 1986-2016, this is what I found (again not 100% sure of every season 1986-01'):
-1996 #1 Marshall (with Randy Moss) (14-0) beat #2 Montana (14-0) (only time 2 undefeated)
-2009 #2 VU beat #1 Montana
-2011 #2 NDSU beat #1 Soft Houston
If JMU and NDSU did both make it, I think it would only be the 4th #1 vs #2 in 32 playoffs since the field was expanded to 16.