There aren't really any cons other than the more body lift, the shorter your shifters get . Thats of course ignoring that fact that all body lifts over 1" look bad . Just my opinion . Could affect center of gravity, but not by much since most your weight is in that tank of engine and running gear.
2nd that...1" is fine and your steering column will absorb that little change...any more than that and you'll have firewall/steering box issues (if you are running stock steering) plus anything over 1" just looks odd on a FJ40.
Just installed a 1" body lift on my SUA FJ62 and noticed very little difference in center of gravity change. Of course my set up is spring under not spring over, but I wouldn't think anything around 1" would create any noticeable change. If you are still running a fan shroud, it may have to be modified for clearance on the bottom, but that should be the only modification you need to fit a body lift of the 1" variety. If it bothers you, you will notice a gap mostly around the front and rear bumpers, but that can easily be fixed.
Hey Woody, where'd my blue faced smiley go? ???