as an owner of a 1994 c280 for 12 years, I can tell you you're asking alot. The m104 straight 6 is one of the most durable, bulletproof, reliable engines ever built. However, not many options for upgrading the power. Though, I can say I've never heard of anyone doing any headwork like you're planning. I bet that would definitely help. Its what amg did in the c36 to squeeze more hp out of it. They also increased stroke (and maybe bore, not really sure yet) by using a different crank to bump it up to a 3.6l straight 6.
K&n is risky. The oil on it easily gets downstream on the mass airflow sensor. That's a pricey sensor.
Exhaust options are out there. The leistritz manifolds are stock and are superb. No idea what kind of gains come from performance m104 manifolds. Probably pricey, though. Everything behind the manifolds is easier to find, and does offer noticeable hp gains. I've heard 20-30 more hp is realistic. I think anyone claiming to have a chip or reprogram for this car is selling you hot air. Never heard of anyone getting any extra power that way. The preupdate w202 is obd2, but there's not much hidden away in the computer.
As for engine swaps, its very very easy. Plug and play. however, only 2 other engines would work: the 3.2 from a 94-95 e320 (240hp), or the very very rare 3.6l from the c36 amg (275hp). Emphasis on very rare. If you found a crashed c36, I'd honestly buy it and use the c280 as a new frame and body to rebuild the c36.
You'd have to break 400hp to cause any trouble with the trannie