What gives power on second gen engine is not only the different intake manifold that will give more torque with the long runner setup, the short runner setup will only use 1 throttle body. I think that the 1st gen intake (2 throttles bodies) gives more horspower to the car. The use of two throttle bodies gives a better throttle response.
I think that most of the horspower from the second gen. engine is from those points:
-The piston weight for the second gen is 438 grams for the A size. On the first gen engine, they weight 515 grams. Total weight lost: -77 grams
-The connecting rods for the second gen weight 647 grams. On the first gen they weight 626 grams. Total weight gain: 21 grams
So the total weight lost per piston/rod is 56 grams for each cylinders. Here you gain alot of hp from the weight lost in the engine.
-The second gen camshaft has the same exhaust valve lift that the first gen camshaft. (.2571 in.) It's another thing for the intake valve lift that is .3367 on the second gen. On the first gen cam it was .3209. (On the second gen camshaft, you have .016 in. more lift)
-The exhaust valves are the same on both engines. On the intake side, valves are different: On the second gen, valve size is 1.4319 in. on the first gen it's 1.3728 in. Valves are .059 in. bigger on the second gen engine and there are 2 intake valves per cylinders.
-On the second gen engine, you will find softer springs. That gives horsepower by the fact that valves are easier to open.
-Compression ratio is also different, on the second gen it's 10:1 and on the first gen engine it's 9.6:1 (obdII)
You can find an aluminium block on the second gen, it's lighter so your hp/weight ratio will be better.
-Driver side have the same bold pattern on the block on both generations. (Even on the 3.3)
-Passenger side is different on the second gen, only 1 bolt is not at the same place. So with a minor mod, you will be able to use the second gen mount.
The exhausts manifolds are the same, they will bolt right on.
By plugging 1 hole you can bolt the first gen. intake on a second gen. head. So you can put the 1st gen plenum on the second gen engine.
On the second gen engine you can also find 1 knock sensor on the block. If you use the 1st gen computer with the second gen engine, you will need to drill a hole to use the second knock sensor. You will also need to swap the camshaft sprocket and the flywheel to get the right timing marks to use the 1st gen computer.