[pblankenbaker]

Here is an example of setting/tracking a start time as you transition through your fire sequence. It is broken out into one private attribute (time the sequence was started) and three helper methods.

NOTE: This assumes you are programming using the SimpleRobot framework.

    // This will be set to the time when the fire sequence was started. It
    // will be reset to 0 when the fire sequence completes

    private double fireSequenceStart = 0.0;

    /**
     * Helper method to indicate whether we are currently firing.
     */

    public boolean isFiring() {
        // When the fire start time is set to a non-zero value, then
        // we are firing
        return (fireSequenceStart != 0);
    }

    /**
     * Helper method to start the fire sequence (call this after a certain
     * button has been pressed during operatorControl(), or call it from
     * autonomous() if you want to fire then).
     */
    public void fire() {
        // Don't start a second fire sequence until the first completes
        if (isFiring() == false) {

            // Save time the fire sequence was started at
            fireSequenceStart = Timer.getFPGATimestamp();

            // Not sure if you want this, but you may want to clear your
            // internal "isFired" flag here if you don't clear it elsewhere
            // isFired = false;
        }
    }

    /**
     * Repeatedly call this method from your main loop in operatorControl() or
     * autonomous(). It should take you through your fire sequence without
     * blocking (requires no Timer.delay() calls).
     *
     * ***WARNING*** Make sure your other code does not block or have delays in
     * it, or this timing sequence may fail!
     */

    public void updateFireState() {
        if (isFiring() == true) {
            // Determine number of seconds into fire sequence
            double secsElapsed = Timer.getFPGATimestamp() - fireSequenceStart;

            // This is an attempt to refactor your original Fire() code
            // to change states based on the time elapsed (but with no Timer.delay() calls)
            if (secsElapsed < 0.25) {
                // State for first quarter second (0.0 to 0.25)
                IntakeDown.set(false);
                IntakeUp.set(true);
                isIntakeUp = true;
            } else if (secsElapsed < 1.25) {
                // State for the next second (0.25 to 1.0)
                shooterLatch.set(false);
                shooterUnlatch.set(true);
                // Hmmm, shouldn't isIntakeUp be set to false here?
            } else {
                // Finished (1.25 seconds have elapsed)

                // Reset start time to 0 (indicates we are done with the fire sequence)
                fireSequenceStart = 0;
                isLatched = false;
                isBottom = false;
                isReset = false;
                isFired = true;
            }
        }
    }

Hope that helps.