HT lead and coil order

OK, so while tiding up loom routes while fitting Samco hoses, i rerouted the HT leads from coil to plugs so nice and tidy.

I had changed spark plugs 2000 miles ago when I first got bike and made damn certain HT caps went back to where they came from

On the bike, the Front HT coil agreed with Haynes manual - front coil is upper spark plug (coil 2), rear coil is lower spark plug (coil 1)
On the bike, the Rear HT coil disagreed with Haynes manual - it states front coil is lower spark plug (coil 1), rear coil is upper spark plug (coil 2).

Now as the rear cylinder lower plug cap will not fit on the upper plug (its NGK aftermarket and fitted by a previous owner),
I am assuming that if the Haynes manual is correct (and Aprilia manual agrees if coil2 is upper and coil1 is lower), then I have the leads wrong way around (as did previous owners).
Before I swap HT caps around to the different cables is the Haynes manual correct for rear cylinder?

As a side question, what difference will it have made over the time I owned the bike?

Thanks

Hi, far from an expert but I have always thought that twin plugs gave more efficient combustion and in modern engines one of them fired a nano second
before the other. so in my humble opinion you will have caused no damage but will have been loosing some efficenticy and hense power on that cylinder.

Jeff

Well investigated further by noting what is on bike from ECU to coils (as received) and the rabbit hole gets deeper!
ECU has had Blue/Green (pin 16z) cut (Map 2 mod)
And the wiring for the four non-earths to the coils is definitely not as per either Haynes or the Aprilia RSV Workshop manual!
On the bike

• ECU26 (orange/white) is going to Front Upper
• ECU25 (pink/yellow) is going to Front Lower
• ECU13 (blue/white) is going to Rear Lower
• ECU12 (blue/yellow) is going to Rear Upper

Got some sorting to do unless this is a "clever" Map2 mod as it appears for both sets of plug leads are inverted, with the upper going to lower for front and rear cylinders