First of all, sorry for my English, I'll try to make myself clear... Here it's:
I have a Honda NX4 engine in a prototype car and I'm developing a arduino controlled shifter with pneumatic actuators. For the up shift I need to do a sparkcut to reduce the RPM and shift without the need of using the clutch, so far I know that I need a PNP transistor to block the signal passing throw the SCR on the CDI(avoiding the capacitor to discharge). But I'm running in a monocylinder engine, and my interest is just retard this discharge, and not missing the cycle. Could anyone help me with this problem?
Ideally you're going to want the arduino to know the RPM. That way you can know exactly how much you should be retarding the timing. You can live without the RPM, but you'd just have to have a fixed delay built in, so it will behave very differently at (say) 3000rpm vs 6000rpm (Eg a 4ms delay is a different angle of retard at difference RPMs)
Either way though, I'd simply inline the arduino with the control wire to the CDI and adjust the signal when you need to.
Eg You detect that you're changing gear, so instead of just passing the ignition control signal through unchanged, you would introduce a delay.
Air shifters on bikes can either use a fuel cut or spark cut to bring down the RPM. Cutting the spark means there will be extra fuel coming into the cylinder and it will backfire as soon as it ignites again which can be cause damage to your exhaust manifold. But apparently it's a little bit faster than doing a fuel cut. Anyway my point is that it might be easier/better to just use a fuel cut. If you're doing a button shifter instead of automatic then you could just let off the gas and avoid the need for all that in the first place but once again it's gonna be slower. If you want to keep your foot down maybe you can just connect the Arduino to the wire coming from the fuel pump or something.
Retarding enough to make a full throttle shift possible is going to dump a massive amount of heat into the exhaust valve area and if the engine is working hard (I guess it is since you're considering full throttle shifts) this is a bad idea. There are pros and cons to fuel cut and spark cut, but if you're running carbs fuel cut is not practical anyway so I'd recommend spark cut. I made a full throttle gear shift controller in hardware using a shift light (for rpm sensing) and a couple of relays and a clutch switch a couple of decades ago but I could never persuade myself to trust it enough to actually use it in anger.