hold light flashing

hey all i have a 1988 mazda 626 turbo with a n/a automatic gearbox from a 1996 mazda 626 gv now with my problem the hold light flashs repeatable but when you turn the car off then back on it doesent flash till you actually start driving the car just wanted to know if anyone has a fix for this as i have searched and havent found anything and i have noticed that when driving the car it shifts alittle hard with a small clunk im not sure if thats due to cv shafts or not but i can hear it allso is there anyway of seating the engine and gearbox in properly just in case the engine and gearbox is missed aline