I did not have to notch out anything. From my understanding the post 96 have a frame modification. Honda dispensed with a frame support in the area of the alternator to make it easier to remove and install the unit. From 1990-1995 0ne has to notch or take off the cover.
The old alternator came out with a couple of twists ,and the new one, I had to make three attempts before I got it to go in. It was installed in no time.
I also alternately tightened the bolts, this brought the alternator to the motor without having to push hard to get the unit to seat.
I did have a duh moment. with regards to securing the alt shaft assembley. I thought I was suppose to use one of the alternator bolts and put that in the bolt hole...but the bolt sticks out a couple of inches and you can't get the alternator out.... I had to search my shop for an 8mm x 5/8" long bolt. Once found that worked perfectly. a palm to the forehead moment.
Who did you buy the 40amp from?