'01 Install Into A '94

This is a father/son project to get him in his first set of wheels. I have an abandoned '94 V6 mustang with a blown engine on my property and we're installing an '01 3.8 Mustang engine to get it back on the road.

Here are some of the things we've found so far regarding this swap:

1. The split port heads came on the '99 up Mustangs and gained approx 40 hp over the previous design.
2. The headers changed design including the locaton of the ball socket. The O2 sensors moved to the H pipe.
3. The fuel system is returnless (I'm guessing also beginning with the '99).
4. The '01 up 3.8 had the IMRC like the Windstar and gained another 3 hp. This requires a specific ECM from '01 to '04. Found one on ebay for $60.
5. Begining in '01 the 3.8 is internally balanced. So we will need the corret flexplate for the trans.
6. The engine harness is completely different. I found one on ebay and it's on its way.

Questions for this audience?
1. Where does the hose from the passenger side valve cover go?
2. Can the bracket for the coil pack from an '01 be purchased seperately? The new engine didn't come with a coil pack and it mounts on a different bracket.
3. Can the return fuel line be simply capped?

Some things we have planned:
1. Install true dual exhaust (expecting a 15 to 20 hp gain)
2. Swap out the rear for an 8.8 with 3.55s and traction lok. It also has a beefy anti-sway bar.
3. Install Mach 1 style front calipers and discs.
4. Install Mach 1 wheels; 17 x 8 front and 17 x 9 rear.
5. Go autox racing!

If anyone else has already done this swap, please feel free to let us know what pitfalls are ahead.

Thanks!
 
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Update:

I found out that the breather hose on the passenger side valve cover goes to the intake tract between the MAF sensor and the throttle body, so strike question 1.

Also, the 2001 driver side valve cover has an improved oil baffle for the PCV valve. There was a service bulletin issued regarding the '99 and '00 valve cover because it can suck oil into the intake and cause detonation and the plugs to foul.

Our DS VC was broken during shipping. We replaced it with the one from the old engine, but in the pre-'99 intake design the PCV valve was on the passenger side not the driver's. So I think we either need to find a replacement VC or maybe we can just take the baffle from the broken VC and install it in the old '94 VC.
 
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The new engine harness arrived yesterday. I tried plugging in the various sensors and found that the connector that should mate with what appears to be a temp switch that screws into the aft end of the the DS head is way on the other side of the engine. Maybe I routed the harness wrong? There's only one of 2 possible ways it can go on since the injectors are laid out on either side. I'll try switchig sides but it looks like one of the EGR switch conncetors may not reach if I do.
 
I swapped the baffle from the broken VC into the original. The difference was only very slight. The old one had a small hole near the outside edge roughly centered between the mounting screws. The new one has a narrow slot right on the edge so it is less prone to allowing oil to get sucked up. The crazy thing is the little screws had SAE heads. Probably the only non-metric fasteners on the entire engine.

Also, I located the connector for the coil and determined I had the harness laid out correctly. I started snapping connectors into place and with the exception of the sensor on the back of the DS head, everything is lining up very well.

Last, the '99 up coil pack does not appear to have a removable bracket like the '94 had, so we'll just have to buy a replacement. Scratch question #2.

There are many interchangeable parts on the '01 to '04 3.8 with the '98 to '08 4.2 truck engine. I've read it's good for another 35 ft lbs of torque, so someday we may do another swap.
 
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In the center of the picture there's a sensor that screws into the back of the head, but there is no connector in the engine harness that connects to it. Is the connector in the transmission harness? Can someone with an '01-'04 help us out?