The two stage Merlins were vastly a better engine than the single stage ones, even if the intercooler installation is less-than-ideal, as it was in Spitfire. The Spit IX was both faster and better climber than the Spit V, if we compare the same altitude oriented versions.
1st question about Merlin: can the engine be mated with extension shaft? The V-1710 was a rather modular engine, with reduction gearbox fully detachable, so the extension shaft was rotating at camshaft speed. What was case for Merlin?
2nd question: what would offer the (presumed) Packard Merlin, vs. the historical V-1710? The best performing types, like the -Q subtypes, were making some 385 mph @ ~16500 ft, military power (1125 HP), with external guns. Without external guns, the speed was up some 10 mph, and at WER (1420 HP), no. ext guns, the charts show more than 400 mph at ~10500 ft. No wonder Soviets loved them.
At 23-24000 ft, such planes were still able to do 380 mph. Mind you, those were almost as fast as the P-51A, and somewhere between Spit V and early Spit IX. It was also faster than P-40F (Packard Merlin, 1 stage).
The V-1650-1 makes the rated power (1120 HP) some 3000 ft higher altitude than the V-1710-85 from the P-39Q (18500 ft vs. 15500), the P-39Q engines having the 3500 ft advantage on their on vs. 'plain' P-39D. So the high altitude performance would've received another boost, while the low alt performance would not suffer, due to two-speed supercharger.
In order for the 2 stage Merlin to be installed, the intercooler also needs to be installed, the best spot being maybe under the belly, the drop tanks going under wings. Wings needing some reinforcements.
The engine air intake needs to be at another spot (side of the airplane?), not being shadowed by canopy might allow for better harvesting of ram effect, esp. if the intake is elongated?
The main shortcoming: would the problematic stall behavior get even worse, with heavier engines installed behind CoG?