pay attention to how the head is tightened to the block, if the mechanic is using his pipe over tommy bar and heaving on it then your engine will be trashed very quick. Its an all aluminium block engine and using a calibrated torque wrench is mandatory. If your mechanic does not have it find one or buy one.
The same is also meant for when the mains and big ends are tightened, they require a torque wrench. Do not use general Rs 50 RTV silicone to seal anything in the engine, Use threebond 1207 etc. Toyo FIPG, Hondabond, Yamabond etc to seal items that require a sealant.
The success of a rebuild is dependant on the quality of work done - you as the owner can dictate the quality of work as its your car. If the mechanic says otherwise - strictly tell him that he needs to shut up and follow what you who is the owner of the car wants.
Swapping out engines blindly from the junkyard is major bad news in some cases. I have known people who swapped in a very nice n shiny g'rantee engine from the scrapyard and its timing belt broke 2000 kms later completely trashing the engine. Be careful with your steps, best be smart with your money - just like what you are doing here.