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These are the upper and lower split-port intakes off my 2000 Mustang V6. They deliver air (from the throttle body), crankcase fumes (from the PCV valve) and recirculated exhaust gases (from the EGR valve) to the two intake ports on each cylinder. Red lines on the photo above indicate the paths of the intake runners (long and short) that feed cylinder number 1. The long runners are tuned to produce torque at low rpms, and the short runners to boost horsepower at high rpms. This article describes a mild port/polish job I did to match the upper and lower intakes and the phenolic intake spacer I installed some time ago. My goal was to improve airflow at high RPM's without affecting the low end torque of my naturally aspirated engine. I tried to open up, match, and smooth the runners without seriously changing their tapered profiles. I did a lot of reading before picking up a tool. Some how-to articles that I found helpful are linked below. I've also listed the tools and supplies I purchased along with their source and cost.
How-To Articles
Tools and Supplies
 I have a Dremel Multipro with a flex-shaft attachment, but it lacks the power needed for porting. I only used it for light work (polishing the runners). For the heavy work I used a long shaft electric die grinder with a variable speed control from Harbor Freight Unregulated, this die grinder runs way too fast (25,000 RPM), but with a variable speed control, it can be slowed to the point that it is useable for porting.
   I bought a new respirator, eye protection, and gloves. If you try this job, please do the same, and be sure to wear them. You'll need some supplies like RTV, gasket maker, and anti-seize. I also picked up new gaskets for the thermostat housing and EGR valve, and a set of new o-rings for the fuel injectors.
Prepare the car
Remove the Upper Intake Manifold
Remove the Lower Intake Manifold
Gasket Match/Polish the Intakes - 1999/2000 model year
 This is the bottom of the upper intake with a gasket in place to show where material needs to be removed (red dye) to gasket match it. Also shown are the two metal posts that are used to accurately align the upper and lower intakes ports. If you use an intake spacer as I do, you need to either glue the spacer to the upper intake, or install longer posts so that they reach through the spacer and engage both intakes.
 Here are the finished intakes. When gasket matching, I extended the gasket profile about 1-1/2" into the runners. I did not gasket match the bottom of the lower intake (right) because I wanted to maintain the runner's tapered profile. You need that taper to promote air velocity through the intake on a naturally aspirated engine. However, I did polish the full length of the lower runners. On the lower intake (right) you can also see where I drilled and tapped a 3/8" NPT hole to accept my Autometer water temperature sending unit.
 Before putting the intakes back on the car, I temporarily assembled them with bolts, gaskets and my spacer to check on the port alignment where they join. You can see at least part of each joint with a flashlight. In the case of the short runner (right) you can feel the joint with your finger.
Gasket Match/Polish the Intakes - 2001 and later model years
 If you are working with a 2001 or later lower intakes (shown above from the rear) you have to deal with Intake Manifold Runner Control (IMRC) butterfly valves that are installed in the lower intake's short runners. At low rpms these valves are closed so that the engine draws air primarily through the long runners. That increases low-end torque. At high rpms the valves open to allow airflow through both the short and long runners. When porting and polishing this model intake you must either remove the IMRC butterfly valves or work around them. You might want to remove/delete them if you plan to install the intake on a pre-2001 car, or if you plan to install a supercharger or turbo and want to open up the runners as much as possible. Otherwise, you should leave them alone. Since I was considering putting this intake on my 2000 Mustang, I removed/deleted them.
  This shows the same 2001 lower intake before and after the IMRC butterfly valves were removed. To do that, I drilled out the screws holding the butterfly valves, and pulled the 5/16" diameter IMRC shafts out of both sides of the intake. There are also some small pieces of spring wire to remove. To plug the holes that remained, I first cleaned them out with carb cleaner, then inserted in each side a 15" length of 1/4" aluminum rod liberally coated with JB Weld. When that rod was hardened in place, I used a hacksaw blade and a die grinder to remove sections of the rods where they crossed the ports. After polishing the runners, it was hard to tell that the the IMRC's were ever there. Another approach would be to weld the holes shut, but I don't have access to a welder. If using this intake on a pre-2001 car, you may also have to drill and tap holes for one or more temperature sending units. (2001+ cars use a temperature sensor on the cylinder head.) You can see in the above photo two locations (pads) where these 3/8" NPT holes can be drilled/tapped. In this picture I've got them temporarily filled with threaded brass plugs.
Reinstall Lower Intake
 Look at Mustang Steve's article on Installing an Intake Manifold. Ford has improved the 3.8L splitport gaskets over the ones Steve used on his 5.0L, so you don't need to glue the gaskets to the heads or use as much RTV as he recommends, but he raises some good points. If the lower intake gaskets are not installed correctly you will get coolant leaks. The location of the 14 bolts (6 long, 8 short) are shown above. Tighten these bolts in two stages using a torque wrench that reads in inch-pounds (in-lb), and following the sequence shown above. (If you don't have a wrench that reads in inch-pounds, divide by 12 to get foot-pounds.). Be sure to put some anti-seize on the threads.
Once the lower intake is on the car, you can use a flashlight to check the port alignment between the intake and the head. The short runners match up perfectly,
but the long runners do not.
Reinstall Upper Intake
 Instructions are here, and shown above are the bolt locations. Ford recommends that you tighten the bolts in three stages, following the sequence shown. Again, you will need a torque wrench that reads in inch-pounds (in-lb) and anti-seize for the threads.
Results
Now that everything is back together the car runs fine, with no coolant leaks. It seems to sound smoother, rev easier and pull harder
at upper rpm's, but that could just be my imagination. My butt-o-meter always indicates an improvement after I've spent $$$ and time on a
modification.
Things I learned while doing this mod
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On the right is a photo I took of the head when the intake was pulled. You can see the same mismatch
between the gasket and the port in this picture. The gasket is installed with alignment pegs, so it can't be the problem.
The problem is in the head, and the only way to fix it would be to port (gasket match) the head too. But that's a project for another day....
I'll have to wait until my next trip to the track to see if I have really
gained any horsepower.