When you "port & polish" the intake system it generally means making a perfect fit (match) between all the openings of the mating parts, making all the individual ports/runners etc. the same size/area (so that there is a balanced airflow) and putting as smooth a finish as possible on all the interior surfaces so that there is as little resistance to the airflow as possible, For example...take the 3.1; at the throttle body and the plenum (upper intake manifold) bore where the T/B is attached, if there is a mismatch, (an offset, lip or a step against the airflow) you carefully remove material as required from the inside surface of the plenum bore so that there is a smooth transition when the gasket & T/B are mounted on the flange. (My '92 3.1 had quite a mismatch there with the step against the airflow) I also had to trim the gasket a little bit.
The bore of the T/B should exactly line up or match that of the bore of the plenum. Use the hole in the gasket as your guide. You repeat this for every other port between the six intake runners of the plenum where they mate with the lower intake manifold and if you remove the intake manifold (lower) you would also do the same thing between the ports of the manifold & the intake ports in the head just upstream of the intake valves. When you do this you also as part of the process remove any flashings and the rough finish (these are cast parts & are not usually finished very well due to cost) of all the interior passages of these parts including the plenum cavity (easy) and all the runners of both the plenum & manifold (difficult) as well as the area just adjacent to each intake valve in the heads. You finish by polishing to as good a finish as you can. It would be better if the heads were removed but I did it without removing the heads. With the heads off you can do more. (exhaust ports, manifold, c/c etc.) The pros would fluid hone & air/fluid flow check these parts to ensure equal flow through each port & runner but this is not practical for most of us. (This is done on the Mustang Cobra for example.) You will have to use hand files, rotary files/burrs, emery cloth/paper, crocus cloth, Cratex wheels etc. Beg, borrow or steal a Dremel with the flex shaft (and any tools/bits that you can get. It is a must. There are some long passages. If you remove the intake manifold & not the heads you have to ensure that the the lifter gallery/head area is covered to prevent contamination as much as possible. I found this impossible to do so I used only rotary files on the heads so that the only contamination was aluminum swarf but no abrasives. I vacuumed out anything that had gone into the area, flushed the area with varsol, dumped the oil, reflushed and then did a quick double oil change with filter after completion & it was running again. I was also removing coke/carbon from my intake valves as well so that I had pressurized each cylinder with air so that I probably had more crap flying around than you will. WARNING....DO NOT remove any more material than necessary. Your concern about the gaskets is valid. The gasket between the plenum and manifold is WHAT WILL LIMIT THE AMOUNT OF MATERIAL THAT YOU CAN REMOVE AT EACH PORT. You will have to use the gasket as your guide when you match up these ports. This gasket is a GaskoSeal type with plastic locators that position it on the intake manifold. Make use of this as a template to determine the amount of material that you can remove to get the exact contour, size, corner radius etc.(Temporarily put the parts together using the old/new gaskets and bolts/bolt holes as your guide. In operation there can be slight relative movement (thermal) between the plenum and the intake manifold. (note the neoprene rubber spacers!
In other words the outside diameter of each port will be just "inside" the inside diameter of the green neoprene gasket material. If you go past (enlarge the port size too much) the sealing surface of the gasket YOU WILL END UP WITH A VACUUM LEAK. DO NOT NICK OR GOUGE THE FLAT SEALING SURFACES OF ANY OF THE PARTS. Protect them with tape if required. The same theory applies to the ports at the manifold to head areas. Also, do the EGR valve boss area as well. You can also remove ("hog out") quite a bit of material just behind the T/B bore in the plenum. I think it was toward the top. Keep in mind the thickness of the material though. Blend any sharp nicks/gouges etc. There may be some minor porosity. Don't get carried away trying to get rid of it. Ensure everything is cleaned/flushed to remove any swarf and abraisives before reinstallation. Removing the lower intake manifold is fairly major. You have to remove the push rods which means that the rocker arms have to be removed/turned aside. You will need a torque wrench & high strength approved sealer for the intake manifold end seals. Mark everything as to their location. The gaskets/gasket kits required are not cheap. On the plus side doing this job along with the K & N drop in (NOT CONE) filter will I believe give some performance gains.