. I understand what you are saying about the pairing of cylinders as #1 and #4 are in the same position whereas #2 and #3 are both 180 degrees out.
When I helped out a guy with a K7 600 that would not start about a month ago, I remember thinking the CKP was not in the position I expected it to be when we pulled the cover off.
As you can see from the picture below, the "wide" tooth on the cam chain side of the engine is clearly lined up with the #1 and #4 crank pins.
On installation of the cam chain sprocket/trigger wheel, the "wide" tooth is aligned with the wide trigger portion of the trigger wheel. Otherwise, when cylinder #1 is TDC, the wide trigger is pointing towards TDC. ("up")
From this picture we can tell that #1/#4 is about 45 degrees BTDC.
The kicker is that the CKP is mounted below the trigger wheel so it would be giving it's long "high" pulse at BTC of cylinders #1 and #4 or TDC of #2 and #3. (I flipped the following cover picture to orient it with the engine picture)
Of course this does not help the OP directly, but it is interesting just when the CKP receives the long signal on each crankshaft rotation. It seems that #2 and #3 get direct pulses for timing and timing for #1 and #4 is interpreted.