I'll try to help out a bit.
1) for the most part the 996 is a very reliable car. That being said, the engines do have some weak spots and there is potential for issues. Those issues are the rear mains seal leaking, which is not a big deal, just have it replaced when you get your clutch changed. On the deeper end of the scale the IMS (Intermediate Main shaft) can fail which results in a catastrophic failure of the motor and finally, on the earlier MK I cars they have some cylinder wall issues that can fail. The occurrences of these issues is a closely guarded secret by Porsche AG and no one really knows how often these things pop up. Don't be deterred from a car with a motor replacement as these cars tend to have new motors from Porsche with the latest update parts in them. I wouldn't walk away from a car with an original motor but having a fresh one is a nice plus in my book. For the most part, it seems that engine failure is a minority of the cars but it does happen so you may want to educate yourself to what your alternatives if it happens. Thankfully, there are now new options for sourcing rebuilt (arguably stronger) motors than ordering a replacement from Porsche but this information is just hitting the forums now. There is much anecdotal information that says a car that's driven tends to have less issues.
2) Working on the 996 is not any more difficult than another car. The only caveat is that much of the motor is not assessable by the rear deck lid but from the underside of the car.
3) Differences in the C4 and C2 aside from the obvious 4wd is the weight difference between the 2 cars and balance. The C4 is a bit heavier and will push more at the limit. The C2 feels lighter and more nimble and is easier to drive with the throttle.
3b) X51 adds a new intake manifold, heads, headers (IIRC) and upgraded oiling system. It's rather an expensive option but I can't speak to the value of it as I've never driven a car with X51. The standard 996 motor offers quite a bit of power already.
3c) You can add on some bolt-ons that will provide an increased performance but will it equal the X51? Probably not but the X51 was around a 10k option IIRC. I'm more in a position to recommend learning how to drive the 996 as it is a challenging car where the BMW is a very forgiving car. The 996 requires finesse and sensitivity to drive it effectively. Your money is better spend in driving schools if you want to go fast. The MK I engines seem to respond better to bolt-ons but you can add more performance (straight-line) with an intake, plenum and exhaust. That will make your car a bit more punchy and slightly quicker. Again, is it worth the money? debatable. I'd go for suspension and schools before adding other items.
3d) The X51 is pretty much maxed and I haven't read of anyone extracting more NA power out of them but I could be wrong on this. Of course there are supercharger options for both motors but those are quite pricey as well. At that point, you might as well go for the turbo.
For background information, I picked a 99 996 MK I even with the higher risk associated with the 3.4 because of the following reasons. MK I Aero kits to me are the best looking of the 996 narrow body (subjective), they tend to be the lightest cars of the bunch and finally, they were offered with a LSD and defeat able traction control vs the PSM that was offered on later cars. These cannot be turned off and will try to fix you if you in the most in opportune times (when you are trying to rotate the car). LSD was only offered in the 99 and the 04 40th anniversary edition cars.
I came from an E36 BMW and have driven virtually all generations of the 3 series including M3's in autocross so I have a penchant/passion for BMWs as well. The 911 is a whole different ball game entirely in terms of experience and driving dynamics of a rear engine car.
Hope this helps,
Pete