Yes, it will phisically bolt up. 4A-series engines parts are interchangable.
But as you already said, the exhaust is different. Compared to the 1st gen, the flange from header to downpipe is different. Where the cast-iron header goes from 4 to 2 pipes, the pipes are behind each other so to say.
On the 2nd gen, the pipes are next to each other (so there is a 90 degrees difference between the pipes)
It's the only reason why I didn't go with a 2nd gen header on my old Corolla. The 2nd gen header is much nicer than the cast-iron cracker of the 1st gen.
Something else to think about
: Are you also going to use the ECU and wiring loom from the 2nd gen?
Most sensors are on the cylinderhead and they do differ between the two generations. So it would be easier to use the 2nd gen wiringloom unless you want to modify your current loom. That would solve the problem with the dizzy too
The 2nd gen might run on the 1st gen ECU (I do not know this for certain!) but since the intake, exhaust, and some of the sensors are different (and the programming of the ECU is different as well) I think you should go with the 2nd gen ECU as well. That way you will know for sure you get the 115bhp the 2nd gen makes.