I'm sorry to differ with you Bighorn, but that's not correct. The production aircraft did indeed have altered exhausts and this added some thrust. The prototypes had a grouped outlet system. However the manufacturer's figures for each model is known and the U.S. tests far exceed the best of those. The higher performance for the U.S. test was due to a combination of higher octane fuel and the engine being in tune to use that.
Regarding the flaps, I have similarly been able to find no data regarding a maximum airspeed for flaps to be deployed. I'm sure there was one in the manual or printed on a decal somewhere but I also doubt it was as low as 164 m.p.h as it is in the game. The whole wing structure is really built around this flap design which was carried over from the Ki-43 (and earlier) from the outset and is a distinctive Nakajima feature. If you inspect the deployment rails and mechanism it implies they were intended to be used for manoeuvring and not just landing flaps. The deployment mechanism is hydraulic and the flaps themselves are a considerable structure. There are four rails per flap.
I conjecture that in real life the flaps might limit your speed once deployed and not the other way around. I once had both flaps shot off when deployed and flew around until my fuel ran out experimenting. It was impossible to accelerate past a certain speed (I'm afraid I have forgotten the figure).
I thought I had a convincing case that the flaps were modelled incorrectly in Aces High but trying to substantiate it I'm now not so sure, but I'll present the info anyway for your consideration.
On the instrument panel of Aces High's Ki-84 is a flap position gauge, below and slightly to the left of the manifold pressure gauge. There is no equivalent for this on the instrument panel of the real Ko (this position is occupied by the oil temperature gauge) nor can I find such an indicator elsewhere in the cockpit.
The Aces High gauge is is labelled 0, 15 and 30 degrees respectively although I believe the pointer does go slightly off this scale at the 30 mark which would be commensurate with the specifications.
However, according to Wieliczko's book, there was a third setting for the flaps which we do not have which allowed them to be extended even further to 53 degrees:-
"The flaps were all-metal and consisted of fourteen ribs. They were placed between ribs 2 and 14 and extended asymmetrically on four guides, with hydraulic control. Their maximum extension angle for landing was 53 degrees, 35 degrees for take-off, and 15 degrees in combat maneuvers". [Nakajima Ki-84 Hayate, Leszek A. Wieliczko, Kagero].
I cannot validate this information from a second source, so I suppose we must remain sceptical. Information is so scarce I think a more convincing photograph would clinch it but I have been unable to find one. There is a picture of the flaps deployed in a position apparently exceeding 35 degrees, but perhaps you can judge for yourselves:-
Flaps at 35 degrees from Aero Detail (in which flap deployment maximum angle is states as 35 degrees).
Flap deployment picture from Wieliczko.
I believe the flap positions may not have been discrete however as they were controlled by lever which actuated a hydraulic valve and might have allowed a variable angle of deployment instead of the fixed positions we have.
Regarding the dive of the aircraft: the flight testing implies that the elevators did become very stiff at high speeds which would be reflected in the game, however the shedding of control surfaces in Aces High is rather inexplicable.
During a discussion of the development of the Mansu produced Ki-116, which was a developmental version of the Ki-84 featuring a smaller, less powerful and lighter engine fitted to an otherwise identical Ko, Wieliczko mentions that this aircraft achieved 800 km/h (497 m.p.h.) in a dive. In Aces High I believe you would lose all of your surfaces in random sequence by the time you reached that speed, even if unloaded.
Finally there is some evaluation of the aircraft for which the source is not cited but which I am assuming stems from the flight testing of the captured Ko (Ki-84-Ia Late Production version (serial number 2366 assigned tail number S17)):-
"The construction of the Ki-84 was very strong and allowed both rapid maneuvers with high overloads and high speed dives".