Interesting.
You say it's getting "noticeably hotter". Have you ensured there's adequate engine oil in the sump?
I assume you're using Motul 7100, 15W50. That's a high-quality oil. I use it too. So the oil grade/quality can't be the issue. But, the volume is also important.
Now, I'd suggest you get hold of an infra-red thermometer, ride the bike two-up for 30 - 45 minutes, then take temperature readings at the sump and near the spark plug (where it threads into the head).
A sump temperature up to 120 Degrees Celsius and a head temp of up to 150 DC is normal. Also, if riding in stop-and-go traffic the head temp is going to be higher - and the sump temp lower - than when riding on the highway.
This information is acquired from owners and experts of air-cooled Harley Davidsons.
Moreover, check the colour of the spark plug. If it's running too lean due to fuel-restriction, it could run hotter temperatures.
The fuel-restriction could be caused by a number of things like air leaks in the hoses and manifolds, clogged fuel-injector, dirt particles inside the fuel pump module's filter/strainer etc. Also, check the air filter to ensure it's clean.
Yet another possibility could be binding brakes, drive-chain too tight and an engine not yet fully run-in.
Oil quantity was the first thing I checked when I first caught wind of the problem but nothing's changed there. It's topped up (right at the top line) and not burning any oil. The oil itself, from a small sample I took from the pan (and of course refilled with fresh) was mint. Barely darkened in 1500km's. Still shows red through the glass as well with no bubbling or sediment or separation.
I did also check the spark plug. First after a few hundred km's since I installed the filter and cover and actually just yesterday (when it got hot again) as well. Pretty much the same as before, no changes and pretty normal to a touch on the leaner side, at least for my liking. I usually had them a bit darker in carburetted bikes but in any case, the EFI seems to be working properly. I have no hiccups, hesitation or anything of the sort. I go for an alternating fuel fill up regime as well, premium/regular.
Air filter's clean as a whistle, too and seems adequately oiled from the factory.
The brakes I did extensively, I have no problems there. Chain's also adjusted and regularly cleaned and lubricated. The bike's got 3500km on the clock so I'm assuming it's well run in by now.
I should note again that the bike gets hot only when with a pillion. When I'm by myself, doesn't matter if I thrash it relentlessly, it never gets as hot. Also, the heat is certainly coming from the engine and not the exhaust or any other part. I can really feel it in my legs!
The thermometer is a good idea but it'll have to wait I'm afraid. So far I've been chalking it up to the increased strain of a small bike with two hefty passengers since there doesn't seem to be anything else wrong with it but I'd rather be on the safe side and pass it on to the next person undamaged!
Many thanks again!