VelocideX & Synto,
Sorry for the delay in replying. I'm currently working on a project and don't have much time to get on the net.
Anyway, I very much doubt that there is any authoritative scientific study which determines the actual absorption rates and resulting bioavailability of MDMA. As we all know since MDMA is considered a toxin, and not a pharmaceutical, there's no interest in this in the traditional medical community. At the same time, there apparently have been some studies related to what occurs chemically when MDMA (a mild alkaloid) passes through the stomach and on to the upper intestine. I'm not very fond of the folks at the NIDA, but based on how other pharmaceuticals react I believe that their description is right on here:
http://www.drugabuse.gov/pubs/teaching/teaching4/Teaching2.html
Ecstasy is a weak base--this means that Ecstasy is likely to "pick up" or accept a hydrogen ion (H+) from the surrounding medium (the gastric acid in the stomach is loaded with H+). Once the Ecstasy has accepted a H+, it has a charged (or polar) character, which makes it difficult to cross a biological membrane. Biological membranes have a nonpolar core, so compounds having a nonpolar nature are more likely to diffuse across the membrane (passive diffusion). Therefore, most of the Ecstasy is not absorbed from the stomach into the bloodstream. Rather, the Ecstasy molecules get emptied from the stomach into the upper intestine. In the intestine the more alkaline environment causes Ecstasy to give up its H+, becoming more nonpolar. The large surface area and the more alkaline environment enable the Ecstasy molecules to diffuse across the membrane into the blood capillaries very quickly.
MDMA requires the alkaline environment of the intestine to switch its polarity back to allow it to cross the membrane and enter the bloodstream. Something that they don't mention here is that the alkaline levels of the intestine change due to many factors (health, immediate diet, etc.). I would wager that one of the reasons people experience differing intensities and dosage to peak times with the same batch of pills has a lot to do with the "current" state of their intestinal tract.
If the intestinal environment doesn't happen to be very alkaline at the time of the dosage, it is very possible that some percentage of the MDMA never looses the additional hydrogen ion which it acquired in the stomach (e.g., it can't be absorbed through the membrane).
In terms of drug bioavailability the rectal/colon route, there is a great deal of pharmacokinetic research available regarding how compounds behave when administered in this fashion. As I mentioned, it is very unlikely that any lab has studded MDMA absorption specifically. But other drug studies that can be used to as a comparison to develop something of an "educated guess" as to what the drug bioavailability may be.
My "guess" is that it is somewhere around 20% higher than when administered orally. Partly due to the fact that MDMA is compromised to a certain extent when taken orally. And partly due to the fact that MDMA is naturally prone to pass through the intestinal membrane via passive diffusion.
The other part of my "guess" is from reports given by people who have tried it, and from my own experiences. There is definitely an increase in intensity when "plugging," and given what we already know about the pharmacokinetics of other drugs I don't think that the intensity is solely due to a placebo effect.