From the 2004 NHRA rulebook:
ENGINE
Must be of a type specifically designed and manufactured for a production motorcycle. Harley V-twin or NHRA-accepted American push rod V-twin, 45-degree case only, maximum 3278cc (200cid). All other 2-valve engines, maximum 1508cc (92cid); 4valve engines 1994 model year and newer, maximum 1429cc (87.2cid); all older 4-valve engines maximum 1295cc (79 cid). NHRA-accepted aftermarket Harley-Davidson or American push rod V-twin engine cases with cylinder anger between 45 and 60 degrees, up to 160 cid, permitted.
There's more but that's the scoop on sizes, go to NHRA.com and read it for yourself.
And before the anti-Harley whiners chime in about how unfair it is for them to run larger displacements and less weight, take a look at how much fairing they have to hide behind. None. Quit whining and watch the friggin racing...