Im also an owner of 2000 VTI Oriel and pretty much happy with its original D16Y. This car have some serious cons but have too much pros. These cons need special attentions like heatups, suspension issue etc.
Coming to your problems.
1- When u changes the transmission it is mandatory to change the ECU of car. Change it to manual one. Im not sure about the D15B manual but for D16Y in the same car uses P2P.
2-There was no need to change the intake manifold by the previous owner as he had kept the transmission unchanged. The intake manifold, throttle body, IACV, of A/T and M/T is different in this engine. So yes now u need to change all three of above to get good mileage, better pic ups, no choking at certain rpms, no rpm droppage under loads (its directly related to IACV).
Any other question and querry will be highly welcomed.