It seems that a lot of us have this problem. Some people get it at stock, others get it after even small mods.
The reason that the problem "seems" to go away if you go to a lower gear is the fact that the throttle plate is opened further and more air is going in at higher RPMs. This tends to "dampen" the effect of the opening EGR valve. At a lower rpm, the EGR opening up is a relative bigger change to the engine than when the rpms are higher. My guess is that Ford and tuners have not yet taken this problem serious enough to fix it. I will try to explain both scenarios.
Stock Ford: Some cars have the hitching problems, while others do not. Every Ford off of the assembly line gets the exact "same" parts and chip. Ford knows that no two cars will ever be "exactly" the same, as there are acceptable "tolerances" for each part. For those that get a car that have parts with tolerances that are at opposite ends of the spectrum on the same car, we will see problems. The ones that get a car with parts whose tolerences are all "close to the same", we will see the freak car that natually outperforms everybodys' in stock form. Each car coming of the line will also run in varied environments (sea level, humidity, cold, etc.). For all of these reasons mentioned above, Ford's computer has an adaptive program to "try" to get the cars to all run the same (to a point of "good enough"). The program can not always compensate enough, but the car will run good enough to not set a code and pass EGR smog tests. These are the cars with "hitching." In my opinion, Ford needs to address their EGR system. It is suppossed to be able to work with NO noticiable effect to the driver or the performance of the engine. They have not designed a system good enough to do this. Until they can write a better adaptive program or they put in components that work smoother, we will not be able to get this problem fixed on stock cars.
Non-stock cars: Many do not have this problem until they change a part. If you read the above paragraph, you will understand easier why this happens. When adding a part, you thow off the "natural balance" of the car and the part introduced may be at the opposite end of the spectrum from the other parts in your car. If the computer was border-line already to be able to keep a smooth running engine while the EGR activated, then the new part (with its own tolerance spec) may push it over the edge. Because the computer's diagnostic program is not accurate enough to be able to "trigger" a problem, the mechanics working on the car find nothing. The problem is not severe enough to the computer for the computer to throw a code. You see, most of the time, if a PCM does not find a problem severe enough to throw a code, then the mechanics equipment will not sense it either. I experienced this first-hand. I brought my KB supercharged GT to an SVT dealer to let them determine if the problem with my car was Ford's or KB's. After 4 hours, they could find nothing, but admitted that there was a problem. They could not blame KB nor would they say that the problem was not Ford's. (very good people at this garage) They did find, however, that the Snap-On diagnostics was reporting random misfires, while all of the Ford testing equipment did not. This tells me that the diagnostic equipment from Ford is designed exactly like the car's PCM and it is not flagging this problem. But because Snap-On is not Ford, they are reporting anything they find. In this case, the Ford equipment considered the issue to not be reportable. In the end, the dealer said that because of the chip tune, they could not go any further because of the overrides. They thought the car was running lean, but because we did not put it on a dyno with a sniffer, we can't be sure.
So, where does that leave us?

Screwed to be exact, at least if you are waiting on a Ford fix. Don't blame the dealer, they can't go beyond Ford's testing equipment (especially for warrenty). But as for the tuners, they have some control. The tuners are going to have to step up to help us because they can control the PCM and some are willing to try things. The most critical change, however, (and in my opinion) will be in the EGR tables. This is a "scary" area for tuners. The gentleman at Kennedy's garage told me over the phone that "tuners would be crazy to touch the EGR tables." Kennedys is a VERY well known KB shop. He stated that they have to be very careful because the car has to be able to pass emissions. OK, I can understand that. So..... give us switch chips that has a setting to pass emmissions for when we get tested. The other "settings" will be for performance and drivability.
I want to mention that Kenne Bell IS trying to help me with my problem.

It just so happens that I also have a pinging problem. They think they have identified the problems and will be getting me a new BAP sensor and chip soon. I will keep you all updated on these issues. In the mean-time, maybe somebody can get their "hitching" car to T&J's shop and let them do a little R&D. I have a feeling that these guys will fix it before Ford will.
I have also thought of one other thing to try if somebody is willing to try it. (I would if I had enough time) It will not screw up the engine, so don't worry about that. Somebody could try to make a "restrictor" plate. A reduced EGR hole going into the intake might solve the problem. Or if it doesn't totally fix it, it just might make the problem so small that most people will not detect it. Yes, this is a "bandaid" to the "real" problem, but we have to try something. In effect, the restrictor plate would make the EGR hole "smaller" going into the intake. This would dampen the effect of the EGR. If the hole is too small, then the EGR sensor will thow a code. Another negative with too small of a hole is the fact that it will carbon up quicker at this restrictive hole.
Some people have already built EGR "blocking" plates to fix the problem. This is not a good idea. This will totally throw off the computer and definately make a code come up. Your tune would also not be good because the EGR tables are relative to the stock parameters that are expecting "some" EGR gases at certain times.
Chewing my cud on the EGR table again, I would like to make a point. Tuners program the non-egr side of the computer. Think about this for a minute. If the changes in the devices (supercharger, timing adjuster, MAF, TB, CATS, etc. etc.) throw the computer off enough that a chip has to be burned to adjust for it, doesn't it seem logical that the EGR will be effected as well? Add-ons (including blowers) make the car more responsive to changes in the air stream going into the engine. If the EGR tables are not updated to account for these changes, then it will be trying to make adjustments at certain RPMS and temperatures for what it believes to be stock parts. I am no tuner and I do not claim to be (and there is a real possiblity that I really don't know what I am talking about

), but I can think some things out logically. Again, I could be all wrong. But if I am so wrong, why has nobody come out with a fix for this problem? In the end, we may need to get a sticky started so Ford will pay attention.
Some people put the screen back in to fix the problem. Thiose people will swear that the screen is absolutely the problem. Others put the screen back in a get NO improvement. Same problem, but it only fixed one of the two. Only..... there NEVER was really a real "fix." The person who fixed their car with the screen mearly brough the car back to stock "tolerances" to where the PCM program could again compensate enough to get the car smoother. For the other guys where the sceen had no effect, his car is still out of tolerance enough where the screen did not bring the car back to spec enough for the computer to make enough changes to get it smooth. However, in both cases, the car ran good enough to pass smog tests. And this is all Ford is concerned about. Ford has to either to make a smoother operating EGR system with finer control, or they need to reprogram their computer so that the EGR can be regulated better. In the mean-time, the tuners need to get one of these "cars from hell" and do some R&D for a "real" fix. If the tuners can do this, they will be able to sell chips not only to modders, but to the average Joe to make his car run smoother. Maybe this will be enough to give Ford a kick in the buttocks so they will help us (and the dealers) out.
Off of my soap box now and Batman flame-proof underware is armed and ready.
