check engine light

i am new here. i have a 98 gt with a new intake manifold. i cracked the old one like many others probably have. the new intake is not the pi but is significantly larger than the old. everything bolted right up plus has same #'s. 1 day after the change check engine light came on. had codes ran and it was a P0401. that is insufiecent flow through egr. i came up with many diffrent variables. iac, bad egr valve, or colant temp sensors. they would effect egr sensor correct? if anone has any suggestions they would be appreciated. also i have a kn filter and 2.5 exhaust with x over and flows. 40 series. thanks

Did you put in the MIL eliminators on your O2 sensors yet? With the Xpipe you will get a Chack engine light if you don't. Plus the Xpipes usually burn out the O2's faster than stock pipes (heat). Do this if you haven't, and then reset the battery/elec system (undo the positive for a few minutes.).
You may ned to remove the EFM (elec fuel management) system and use a custom system? I am having mine removed and The shop is custom programming a replacement chip/system.
TK

i haven't put mil elims on yet. i don't know anything about mustangs. if i burned out the o2 sensor would that give me the hesitation. it only happens around 1500 2000 rpm and 40 to 50 mph. how much is the sytem you are talking about? thanks

i haven't put mil elims on yet. i don't know anything about mustangs. if i burned out the o2 sensor would that give me the hesitation. it only happens around 1500 2000 rpm and 40 to 50 mph. how much is the sytem you are talking about? thanks

The MIL's are 60$ and you can plug them in. There are several different brands.
You may also want a good tune done to you car after that manifold install.
The Chip upgrade can cost from 200-500$ depending what you need. Go to a Mustang shop in town and ask them.

i guessing you have a 4.6 . these engines are very very common for the passage between the intake and egr to become plugged with carbon . remove the upper plennum and check to see if the passage , hoses or plennum is plugged