Getting agrevated with this car, tranny question

ok i am on my last nerve with this 2001 acura integra gs.. we have sunk 1000s of dollars into this car and still have problems with it running correctly.. this car has intake, exhaust, stage one crower cams, aem cam gears, ud pulleys, unorthodox crank pulley, pressure regulator, hi flow cat, header, but it is an automatice but still, before we put the stage one cams in the car ran a 10.4 without nitrous in a 1/8 mile, had decent take off with the cam gears set at 20 degrees advance both of them,,, the car ran well... but the timing jumped and then we installed the stage one cams in it and now the car barely runs 10.9 in the 1/8 with no bottle, the car has nitrous but want to see what it will do with no bottle, now with all this the car runs worse now then it did stock it seems... could the transmission need serviced, could the tranny slow down the car if it needs to be serviced with new filter and fluid... .i am on my last leg i dont know what to do next, this car used to outrun si 's but now i dont believe it would PLEASE HELP......

by the way i have the gtech dyno on my dash to help me tune but i have exhausted my ideas..... do we need anything else to make this combo work or will the stock ecu handle all these changes..... do we need a bigger fuel pump please give me all your info that you guys have, this is my wifes car and it is her baby but she is getting very angered about it not running right
thank you
pure evil kustoms