I have a 95 and 00 long term, and flipped a bunch as well. They both have been super. 2000 gets you an air pump and pre-cat manifold. This causes issues for dropping the front exhaust flex pipe; the heat from the pre-cat rusts the fasteners to dust. Though I suppose a similar year twin cam would have this issue. My 2000 has an EVAP leak that goes away for months then comes and goes. I suspect a canister purge solenoid. The newer your car, the more potential OBDII headaches you may encounter. The 1996s in particular throw a "cam sensor" code that's bad coils/ grounds/ ignition wires.
The 2000 with Motorola PCM at least seems more linear/ smooth in accelleration. I suspect they did something to the knock sensor/ timing curve to acheive this. The downer, in stick shift world, is a lenghtly 2000 RPM between-shift "dashpot" idle that's not on the older cars.
Exhaust ports on a 2000 head are way smaller than previous but somehow (cam?) makes the same HP.
They say the 2000+ pistons are better; a better rod ratio and finally some decent oil rings. My 2000 consumes/leaks a tolerable amount, maybe qt in 700 miles at 195k. My 95 got a ring job at 175k when burning was 450 miles per quart.
Somehow the twin cam motors can smoke like chimneys and still run all right. The SOHC ones get into knock retard and get very doggy. The twin cam puts the spark plug in a technically superior central location.
If you want economy, make a mongrel of a twin cam with MP2 sohc tall geared transmission.