You need to realize that each time you reset it, the computer reverts back to the inital A/F maps. After it learns from running it will run somewhat better. This usually means the computer is GOOD.
In situations like this, it's sometimes best to put the stock intake back on and make sure all the hoses are hooked back up. If it runs OK, there was a leak. Look for any differences in the two setups. The hose from the valve cover to the resonater is required.
If it does not run better, either there is still a leak, or perhaps you damaged or unplugged something. The IAT will give a CEL if it's not hooked up but it will not make your engine run really bad.
You do not need a chip just for an intake tube.
