Your rhino will be able to run "ok" with the MSD, it's just not ideal. I ran an 11:1 piston with the HC3 and MSD, Two Brothers V.A.L.E. dual exhaust,
but at the time the TB wasn't bored. Depending on who bored the TB, you could have problems getting it to idle right, common problem, I wouldn't blame the MSD.
Other people on here know a lot more than I do about rhino's, but since you haven't got a reply...
I'll list my findings that I had on a setup similar to yours.
1) You are right, the MSD is 2D mapping. The mapping is based on RPM and not RPM/TPS. This is a problem as your right foot can be in a lot of
different positions at any given RPM and the fuel requirements will change based on that, but the MSD won't accomodate. So it's as you assumed,
the 2D tuning will allow you to dump, say, +10 at 4500 rpm, but whether you're on the pedal hard or half way at 4500, the +10 never changes, but
the fuel requirement would. It'll still run "ok", but you're leaving power on the table...
2) Again, you are correct about the 2D mapping of the MSD when based on ignition timing also. It can generate you a 2D ignition map, which is also
not ideal, but works "ok". The solution I use is a Dynatek DFS7-26 programmable ignition. The curve you can generate on that is more 3D, thus a
better solution. If your timing curve cannot be made somewhat accurate, as is the case with the MSD, you are leaving power on the table again.
3) The HC cam you're using is a long duration cam as opposed to the cams like the Megacycle 2 or 4 as well as the Web 4 which are high lift cams.
Your HC3 likes compression to generate power, and you already have an 11:1 piston, but I have to ask... What piston? The JE 11:1 is ok, but
doesn't have a corrected deck height, therefore sits down in the hole too far to be a somewhat accurate 11:1 ratio. Same goes for the CP 11:1.
Not a big fan of the Wiseco 11:1 for the rhino, and it also sits down in the hole too far. Soooo.. I think the key is to buy a piston with
a corrected deck height so that you can get as close to the 11:1 ratio as possible if you still want to run on pump gas. If not, go with a
bigger ratio. I think (don't quote me!) CP's new 11:1 pistons are a corrected deck height, and you would still be safe to run a 11.5:1 corrected
deck piston on pump gas (premium, of course). Without good compression ratio numbers, you're leaving power on the table.
4) The HC3, even properly compressed, doesn't have the bottom that the MC2/MC4 or Web4 have. So now you have to clutch your rhino according to the
new powerband of the cam. I can only offer a few suggestions on this... Since the cam you have moves the band higher, you're also running tires
a bit taller than stock, maybe look into stiffening the wet clutch springs. This will make the rhino's wet clutch engage at a higher RPM, about
3000rpm. Which is good, as the cam really does not have much below that. You could go with a heavier spring, a lot of people run the gold EPI
spring, but I really think the key is the primary weights. Obviously you will need lighter than stock... How much lighter, well, there's the
rub. I can't guide you without running your exact setup (even elevation plays into this).
5) RPM. The MSD is good at one thing: it can move the RPM limit wherever you want. And you want up to 8000. You could move it higher (say 8500rpm)
but these cams start to drop off after 7500-8000 rpm anyways.
6) To get a "somewhat" accurate fuel map, I'd suggest a Power Commander 5 with the Autotune. It does 3D fuel mapping (as good as I've seen for the rhino)
The PC5 costs less than an MSD, but when you add the autotune, it costs more. But it does more. The problem is it doesn't bypass the rev limit. I don't
think you'll get 8k with it. Not a big problem, since you have the MSD, you could leave it connected to the factory ECU if just to bypass the rev limit.
This works. You zero out all the fuel/ignition maps on the MSD, set the rev limit to 8k, plug in the PC5/Autotune normally and now you have an RPM
limit where you want. And be able to fuel map with the PC5 for it.
The PC5 isn't perfect, but it does offer pretty good RPM/TPS mapping for the fuel. For the average guy, it can totally eliminate dyno tuning the fuel map.
The ignition mapping though is a different story, you pretty much need to dyno tune for that to be close. Going back to the compression/piston issue, if you
are invested into it for too much money, you could still use your existing piston but get more power out of it by measuring how far down in the hole it sits
at TDC and shave the jug to correct the deck height. But this is a one way street, if you bought another piston, one that had a corrected deck, your jug would
be too short. Maybe you could play with extra gaskets to add thickness, but that becomes a game.
Not sure if I helped, but I think I've rambled on long enough!