01 eclipse Gt

Okay so I been having a problem for about a month
now and I'm lost. I have a 2001 Mitsubishi Eclipse
GT.  With 165,000 miles on it. Okay so here's what's
going on. Since I bought the car it had no heater,
and no ac and the check engine light stayed on
because of the egr valve. But the car ran fine so I
never worried about it. Well a couple months ago I
decided I was gonna fix the heater core and did a
flush on it. I had to cut the old hoses off because
they were stale and practically melted on there. Did
the flush and while doing this I knocked the air box
off the intake tube... I thought nothing of it and just
plugged the tube where the air box went. Well after
about 4 miles of driving my car threw a check
engine light and started bucking like crazy. So I
went and got the light checked and they gave me a
couple codes from egr to multiple cylinder misfire
and some kind of egr solenoid. I replaced
everything.. plugs wires distributor cap, rotor bug,
the air box on the tube and did all the check engine
light went off for about another 4 miles and bam.
The symptoms came back and now there is a new
set of codes. Manifold different pressure, intake air
pressure, intake air temp, and the misfire and I don't
know where to go from here. I feel like it has to do
with a vacuum leak. I've done hours and hours of
research and these cars have very sensitive intakes
but I've done it all.. maybe a vacuum line? My dad
thinks it could be the Ecu but I don't want to believe
that. Have you guys heard of this or have any
advice on the next step I should take?