What parts should be replaced when getting a used "low mile" JDM engine swap, if any?

nothing, if you trust the miles. maybe pull a few things like a plug to see if the miles seem right.

definitely clean the egr circuit and think about an oil catch can.

might be a good time to reseal the timing chain adjustment cover

 

Water pump, T-stat since its already out. Yours is old, and you don't know when the last time the one on the JDM motor was ran.
Valve cover gasket since it's easy why the motor is out.
Oil pan reseal/swap if the one on the JDM motor is dented from storage.

 

I'll be doing something similar in the next couple of weeks, except using a salvage yard 2014 engine with 80K. My replacement parts list is pretty extensive:

AISIN WPT190 Water Pump
AISIN WQT001 Water Pump
AISIN ACT002 (ACT-002) Coolant / Antifreeze
AISIN ATF0WS (ATF-0WS) Transmission Fluid
DENSO 3444 Spark Plug
DORMAN 095156 (095-156.1) Oil Drain Plug Gasket
FEL-PRO 72565 EGR Gasket
FEL-PRO 72636 EGR Gasket
FEL-PRO 61711 Throttle Body Gasket
FEL-PRO 72694 EGR Gasket
GATES 34707 Thermostat Housing / Water Outlet
MAHLE MS19724 Exhaust Manifold Gasket
MAHLE MS19723 Intake Manifold Gasket
STANDARD MOTOR PRODUCTS VG250 EGR Gasket
STANDARD MOTOR PRODUCTS V512 Positive Crankcase Ventilation (PCV) Valve
STANDARD MOTOR PRODUCTS EGV1235 EGR Valve
STANDARD MOTOR PRODUCTS TX221 Temperature Sender / Sensor

 

I hope swap doesn't include ECU otherwise you'll have to bear speed limiters (Max Speed and Cruise speed limits)

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I left the JDM water pump Tb and AC comp. All newer than mine all looked better than mine. Saved everything.. of course new spark lugs but what came out looked damn good.