You will need to have the PCM's programming changed if you use a N/A 3800 now and then later put a turbo on it. You cannot use stock 3800 SC programming on an N/A engine; it won't work right. I wouldn't even use stock 3800 SC programming on a turbo setup; especially if you are going to slap a turbo on your L36 N/A engine. The ignition timing settings won't be correct and I doubt neither will the fuel. After you install the turbo setup, you should really have a good, hands-on tune done to your PCM to make sure the settings are 100% compatible with your build. Failure to do this can be asking for trouble.
Having said that, I
wouldn't recommend turbocharging an L36 (or L26) N/A engine, period. These engines have weaker internal parts than the SC engines and they also have higher static compression ratios than the SC engines. The higher compression is going to make the engine more prone to suffering from detonation when you throw boost at it; and when you couple this with the weaker internal N/A parts, you create a higher probability of catastrophic failure occurring. Justinbart had a turbocharged L26 engine and it chucked a connecting rod out the side of the block not too long ago while he was driving down the highway. While it did last an amazingly long amount of time, it finally failed on him when he didn't expect it - which proves these engines aren't that durable when you put boost on them nor can you predict when something like a connecting rod is going to fail if you overload it. You may not be as lucky as Justin (and your engine may not last as long as his did). I can tell you if you don't have a proper tune on that PCM you are using when you slap the turbo on - it probably won't last a week.
My advice would be to go ahead and do the L36 swap now (if you already have the L36) and enjoy it until you are ready to do the turbo. Doing this will allow you to get your mounts and wiring built and all the bugs worked out of the swap while you are waiting on the turbo upgrade. Then, when you are ready to do the turbo, I would pull that L36 out and install (at the very least) a stock L67 or L32 shortblock topped with whatever heads and intake you plan on running with the turbo. If your budget allows, you can build up the L67/L32 engine you plan on using with the turbo to suit your performance needs.
I'm sure other people will disagree with me and they'll say you can turbocharge a stock L36 all day long. They are entitled to their opinions but that's all they are. It is a proven fact that N/A 3800 engine internals aren't as durable with boost as the SC 3800 parts are. And you need to ask yourself if you are willing to roll the dice with your car, or not; based on someone's opinion posted on an internet message forum. After all, it is your car and YOUR money funding this project; not theirs. You certainly don't have to do what I suggested either but I just wanted to make you aware of all the possibilities and potential pitfalls.
I know N/A 3800's are cheap, but the labor to swap them out isn't free and neither is the towing bill if it decides to puke out on the road.
GOOD LUCK!
-ryan
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OVERKILL IS UNDERRATED
Custom GM OBD1 & OBD2 Tuning | Engine Conversions & more | www.gmtuners.com[This message has been edited by Darth Fiero (edited 02-08-2012).]