Yeah I've seen some weird results with the fenderwell headers also. I've run them on the dyno before and had the power curve look funky. I never thought that having the primary tubes too long would cause such a power loss but evidently it does. I had a 505 on the dyno the other day and we tried a Weiand tunnel ram on it. The tunnel ram cost the engine over 100 hp. The long small runners just choked the engine. So sometimes stuff that looks okay really doesn't work.
