Let's go through what affects cold running of the motor.
1) MAFS. You've already cleaned it, see if you can get the readout of the temperature it's providing (should be PID 010F). If it's close to ambient when the engine's cold that's good, but not definitive. Let the engine get warm (bonnet down, why not take it for a drive). In normal suburban driving the intake air temp should sit somewhere in the 50-60C range (with a snorkel, it's probably a bit higher without one). Above 80km/h it should get back down to around ambient. If your MAFS behaves like that it's probably fine, if it doesn't then it might be faulty, see if you can borrow someone's. At $400 a pop it's too much to throw on a maybe.
2) EGR valve open. Easiest fix is to block it, the 2010 Thai build shouldn't have a problem with it.
3) Excessive blow-by. Usually the result of piston rings gumming up, but sometimes also from worn bores, broken rings or misaligned ring gaps (they're not supposed to be lined up nicely!). Disconnect the PCV hose from the air intake in front of the turbocharger, block the inlet where you removed the hose and aim the hose downwards towards the ground. Now cold-start the engine and see how it performs. If it works well with the PCV disconnected, try some high-detergent oil, or oil additive (like
this one from Supercheap - I don't mind Liqui-Moly products, they definitely work).
4) Air in the fuel lines. Actually common in the D40 after a fuel filter change, even by the best mechanics. They're really finicky, you have to properly align the central O-ring which has to be perfectly seated. If a little air gets in, it will make fuel flow erratic until the pump can draw the bubbles down. After an extended period of inactivity, it will be difficult to start. Solution: refit the filter paying extra attention to the pesky O-ring.
You've already checked the other stuff (SCV, CAS, fuel pickup). There's not a lot else, although checking the idle speed would be good. It's supposed to hover around 750rpm.