Autocockers require to be timed after any new components are added to them relating to the trigger, frame, three-way, or firing assembly. The process of timing is called as such because that is essentially what you are doing, adjusting the timing of events in the marker (a certain amount of time elapses between the pressureization / depressureization / repressureization of the front end servos and the actual firing of the marker). The way the Autococker works is actually a finely-adjusted connection between its pneumatics and the trigger, so they must be set to work well with each other. Basically when you time the Autococker, you are adjusting the time when it fires and recocks during the trigger pull.
What to Adjust:
To time the marker you adjust two components of the pneumatics: the length of the searlug and the length of the timing rod. The searlug sticks down from the hammer, attached to the rear cocking rod, and is the component that is released from the sear when the trigger is decompressed, firing the marker. The timing rod is the linkage device that connects the three-way shaft (the rod inside the three-way) to the trigger. It actuates the three-way valve servo; it controls how long the two parts of the ram piston remain pressureized. Making the searlug stick out less will prevent it from ever hooking on the sear, producing the same result that would occur if you held the trigger down while cocking the rear cocking rod (when you pull the rod back and release it, it will spring back into the uncocked position). This is known as a farting Autococker because of the clapping noise it produces. If the searlug sticks out too far, the marker won't cock because you won't be able to pull the cocking rod back far enough for it to get over the sear (the sear will actually block the searlug from moving behind it).
Adjusting the timing rod so that it is too short will prevent the marker from firing because it will never allow the hammer to strike the valve (because the backblock recocks before it gets a chance to fire). If the timing rod is too long, however, it will not bring the cocking rod back fast enough for it to catch the sear when you release the trigger. You will also experiance problems due to the bolt not giving the paintballs much time to load (the bolt will recock late into the trigger pull). Keep in mind that adjustments to the timing rod depend on if you are using a slide trigger or a swing (hinge) trigger. If you have a swing trigger, just take the information above and reverse it, so if the timing rod is too long it will recock the marker before it fires, etc.
Some aftermarker three-way valves are also adjustable. If this is the case, then you can adjuse the three-way instead of the timing rod, which most would agree is easier to do because adjustments to the timing rod require you to use allen wrenches, whereas adjusting the three-way can be done with no tools.
Timing Process:
Assuming you want the shortest trigger possible, the method to choose is to adjust the searlug so that it fires early in the trigger's pull. Then adjust the timing rod so that it recocks the backblock shortly after the marker fires. However if trigger pull is not a variable in the process, you can compensate for a long searlug by lengthening the timing rod. This will provide additional time for the searlug to catch the sear that normally wouldn't have been available. However, there are working limits to the searlug and timing rod, so sometimes you will not be able to compensate by adjusting the other component because it has reached its limit.
If your Autococker farts when you fire it, try to manually cock the marker by pulling the rear cocking rod back. If this cocks the marker, you can easily adjust the length of the timing rod to eliminate the farting. If the marker cannot be manually cocked, though, your problem is either with the length of the searlug or the sear (it may not be sticking up far enough to catch the searlug).
As said, each time something is added that effects the firing you will need to re-time the marker. This means any of the following parts: trigger frame, trigger, timing rod, three-way, three-way shaft, front block, backblock, bolt, bolt pin, valve, hammer, searlug, cocking rod, linkage arm. If you have never timed your Autococker or never seen it done, I advise that you see someone do it first just so you don't end up wasting your time trying to figure out how to time yourself. It really isn't too complicated so that only certified airsmiths can do it, however it always helps to consult an expert.
Certain electronic or electropneumatic conversions, such as the PGI Firestorm, Raceframe, or Eclipse E-Blade, will have electronic settings to complete the timing process. If the conversion is only electronic, meaning the marker still has a sear, timing will be a lot simpler because it eliminates the guesswork and allows the only setting to be how long the bolt remains in the open position.
To view some various autococker aminations that may help, go here and scroll down to where it says "downloads." Specifically, download the file "actsim," it is a timing guide of sorts that will probably help you to understand how it works if you don't (this is the first download available...sorry if you can't read German). You will need WinZip to view these files.