Here is a pic of the transfers. The 1993 cyl is on the left, the 1998 on the right. The flash makes it hard to see the difference in the tunnel widths, but the 1998 is about 1/8" narrower. You can also see the 1998 upper transfer ports are much larger than the 1993.
View attachment 587741
All my observations were made by measuring ports and port placement with calipers. Multiple measurements were made to ensure accuracy, then recorded. Intake and exhaust port measurements were taken at both the cyl wall, and the external faces. I also measured the cylinder depth at multiple locations on the 2 cylinders, with the variance between the 2 cylinders being .004" (2.796" vs. 2.800") The squish band-to-base measurement was consistent on both cylinders regardless of where measured.
Exhaust ports on both cylinders were within .010" in both height and width at the exit. The 1998 cylinder was .017" narrower and .021" taller at the cylinder wall.
The intake port on the 1998 was .018" narrower and .020" shorter at the inlet. It was .072" wider and .010" shorter at the cyl wall.
I am going to be away for close to 2 weeks but when I get back I will bolt these cylinders on and set the squish by shimming so they are both the same, then get some timing numbers. I am sure that will mean more to porting guys than my measurements.