New battery fully charged. Starter in good working order. No spark at any time on the top two cyl.
Yeah but how about the interconnect wiring. When starting that engine you need about 150-200 amps....maint. manual quotation. at 12v divided by 200 amps, the tolerable resistance in the circuit is essentially zero!
Get a voltmeter and check the voltage at the starter red input ⅜" terminal and ground at the metal band on the starter , or starter case if metallic.....or engine block...easier to get to. Crank the engine over and if you don't have 10v or better at the terminals while cranking with a new fully charged battery of adequate amperage, time to check your wiring for corroded (usually) or loose connections.
Usually after cranking attempts that extend over a period of time, the place where you have a bad connection will be warm to hot...reason is resistance of the connection squared times current is power dissipated like in a light bulb and things get hot. Take all connections apart, clean them up and put them back together with adequate torqueing...want them tight but you don't want to be stripping any threads.
I realize that the supply voltage doesn't differentiate between which plugs get voltage and which don't. That's a different problem. I had the 3 cyl 90 and it didn't start well when I had a bad CDI which wouldn't fire a plug. If you lost 2 in starting, you may have your problem. I know of the 2-4-2 thing with the 4 cyls, but don't know if the fuel starvation of the bottom two is also when starting............I never liked that thing and that's why I went with 3 rather than 4 cyls.