4.o stang

so I have a 2005 mustang v6 4.0 manual that we had to change the head gaskets and thermostat housing because the coolant started leaking into the engine. the cylinders and the oil were all filled with coolant and some people tried to tell us it could have been the intake manifold but after taking it apart we found nothing wrong with the intake and we cranked the engine a couple of times without the intake manifold to see where the water was coming from and it seemed to have been leaking in through the two middle cylinders so we proceeded to taking out the heads and changing the head gaskets. after changing it and getting it back together we decided to crank the engine again but without the intake manifold to see if it would leak again but it seems that the engine isn't leaking anymore. so after we got everything back together making sure everything was good we tried turning it on but the engine just cranks and won't start up. my brother has a theory that it would have been that all the sensors are messed up because we were cranking the engine without a lot of things connected. he thinks that just taking it to get all the sensors reset should solve the problem but he's not entirely sure and he also doesn't know much about ford he's owned and worked with Chevys most of his life. so if anyone has any ideas or if they agree with my brother that would really help thanks.