UPDATE

well i decided to take out my k+n intake out and put my stock box back on to see if there is a change. well, there was a change and the start up issue went away. but another issue arose. i was on the way to my girlfriends when i noticed at a stop light my truck was shaking like it was about to shut off. at the next light, it shut off as soon as i hit the brake. and from there on, every time i hit the brake the truck would completely shut off. my idle was so low that the tiniest bit off the gas it would die. so to make it to her house i had to keep one foot on the gas and the other on the brake to keep it on. made it to her house and parked it. called my mechanic to come and check it out and when he gets there, its running completely fine (go figure).

i drove it to the garage from there to take a look at it. we adjusted the idle so it case it dropped, it wouldn't drop to low and shut the truck off. I made a suggestion that maybe the ecu might have adjusted to the intake and screwed something up. so to test my theory the next day i ordered an ecu cheap off eBay and installed it as soon as it came in. worked fine and the truck seemed to run good but the check engine light went on. i get the code pulled and from what i remember it was "manufacturer specific error". my mechanic told me it had to do something with a back up battery which i didn't understand. so i was like whatever, changed it out today and put my stock ecu back and its running fine so far (knock on wood). the lowest the idle has been at 600 rpm's in "Drive
" and about 750 -800 in park. this weekend I'm getting my timing belt done and having the 4runner looked at for any possible flaws. I'm going down to new york for thanksgiving and i need my 4runner to be reliable. man with all these little problems, i feel like giving up my truck and getting something else but Ive put to much work into it to just get rid of it. hopefully it all works out though. wish me luck guys.