also had an engine transplant from 2CT to 3CT(supposedly from a Toyota Sports Van/Picnic) for my 1990 townace super-extra back in 2007...still also working out the vacuum lines but got some help from www.townace.com, just search thru the topics....

for the shifting, the auto tranny oil does need to reach operating temp before it readily & smoothly up-shifts. Have noted that the tranny oil heats up quicker when moved thru the gears (this was also explained to me when I had the tranny oil changed). as per experience, speed is the critical item needed to upshift to higher gears....

BTW...did your 3CT engine have the same height as your orig 2CT? Mine fit the engine supports exactly but was taller so I had to jack up the engine covers 3 inches. Had to have an additonal metal sheet fabricated to cover the gap....