Dave, the sub-floor is thick enough, the thing to check check is that the floor joists are no more than 16" oc. The toilet can be delt with by inserting an extension flange, though this may not be necessary with 1/4" backer. Oak or marble transitions are available to match the floor heights. Baseboards should be removed before installing new flooring. My favorite tool is a Vaugn Super Bar. Sometimes a flexible putty knife is helpfull to first slip behind the baseboard then work the bar between it and the wall.