You'll need to do i diagnostic test to see what fault codes are in the ECU. http://www.toyotagtturbo.com/forums/showwiki.php?title=EFI+self-diagnosis+system Beat me to it lol.
Do it when its slightly warm. Plenty of wd40 or whatever, use a bar with a single hex 14mm to crack the nuts. Dont over tighten the mani nuts either or you might crack the head. Unsure of torque settings, but dont go mental
If you are sending it to a top tuning company who are ment to know their shit then i cant see why anything would have to go wrong. Providing parts are up to scratch etc. Can see why Chris isnt happy, would you be ?