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It appears whoever drilled the upper holes did not use the BIA standard.
http://www.whalercentral.com/articles...icle_id=82

There is a standard pattern for drilling motor holes that all manufactures follow these days.
I suggest you look at the drawing again and you will see that the upper holes are drilled 1 7/8" from the top of the transom.
Yours appear to be around 3 1/2 inches down from the top. Not even close to standard.

There is NO difference between Yamaha, OMC, Honda, etc. They all use the Standard BIA mounting pattern.
Yes, the holes on the motor brackets are spaced 3/4" apart. Thus raising the motor 2 holes results in 1 1/2 inch raise.
All motors on a 16/17/ classic hull should be mounted 2 holes up. Some motors should even be mounted 3 holes up with the right prop.

You will need to drill the upper "Black" holes and the lower "Green" holes so you can mount your motor using a modified BIA standard.
The lower holes being modified in location.
The upper holes following the standard.

Use 1/2" diameter plywood plugs from 3/4" or 1" thick plywood and epoxy to fill the holes.
See this article we have in our Reference section.
http://www.whalercentral.com/articles...icle_id=62