An improved method and apparatus for controlling and implementing instructions in a pipelined central processing unit (CPU) or user-customizable microprocessor. In a first aspect of the invention, an improved method of permitting programmer control of jump instruction interlocks is disclosed. In one embodiment, a minimum of one cycle is required between an instruction that sets flags and a branch taken as a result of those flags; an interlock is used to detect a branch preceded by an instruction setting the flags to ensure that the instruction immediately preceding the branch can not affect the branch outcome. In a second embodiment, a jump instruction following a flag setting instruction whose flags may affect the outcome of the jump is stalled until all flags are set. In a second aspect of the invention, a method of synthesizing a processor design incorporating the aforementioned interlocks is disclosed. Exemplary gate logic synthesized using the aforementioned methods, and a computer system capable of implementing these methods, are also described.