Thanks for the thoughts guys!
Here's some more info.
I'm sure the Graves were sealing well. I had suspected exhaust leaks on the collector pipe as well as the joints between the cans and collector, so I removed everything at one point and placed a seal of high temperature RTV in the joints. Good stuff, approved for use in industrial gas turbines. After doing so, I let things sit for a couple of days to cure and went reiding. There were no leaks as the outer-most seal of RTV was never broken through on any joints.
I was also concerned about the fueling with the Graves, so I had my bike Dynoed an a custom map developed. Everything looked good as far as that was concerned with the Dynojet F/A reading spot-on with the custom map. I have always reapplied the correct map when changing exhaust with my PC3, so there's no trouble there.
I also agree with the sentiment posted here that if cats were the problem, then every bike with non-cat aftermarket exhaust would stink. One other thing that occurred to me as far as this is concerned is the SAS system. I have also removed that and have never attempted to reinstall it throughout this investigation (it's a bitch to deal with). Since the whole purpose of that is to burn the unburnt hydrocarbons immediately following the exhaust valve, maybe that is a part of my problem. I wonder if anyone here can comment on that. Does everyone with the SAS still installed smell like roses, and avyone who has removed the system compain of stench?
I'm also not entirely sold on the idea that the Graves exhaust aren't entirely suited for the SD. For all intents and purposes, the Graves are open pipes. The throat is so large on the cans and the baffling so non-obstructive that there can't be that much of a difference between the Graves and a straight piece of pipe. I've got a decent amount of tuning experience with carbs and I have come across situations in the past where an engine was flat-out impossible to tune properly without a decent amount of backpressure present in the exhaust. This also links to a problem that I have always been disturbed by with the Graves. This is hard to put into words, but here I go. I have owned several other twins and I have listened to several sound clips of SDs with exhausts other than Graves, and the exhaust note on deceleration is very crisp with very distinct combustion pulses. Kind of like b-r--r---r----r-----r------r. My SD with the Graves, with a stock map, with the PCIII site map, with an Akra map, with a custom map, with my experimental tweaking, has always had more of a 'blatty' sound when decelerating. In many ways, sounds like an outboard motor exhausting under the water. Kind of like blap, blugh, blugh, blugh, blugh. I've heard that sort of sound before, and it was always on Harleys running drag pipes, and you could never tune it out. Kind of the same situation on the SD with Graves, as Graves are pretty much a drap-pipe setup.
So as I'm writting this, I think I should call it quits, suck up the cash loss involved with ebaying the Graves, consider the cost of my dyno session a loss, and possibly someday having a go at a different set of aftermarket cans.
Sorry of I'm rambling, but I've honestly never found myself in this situation before, and I'm not sure how I'm here now. I don't know if I should be frustrated about the mods that I've done (many others have done the same), the SD fueling and management system (not everyone has problems with it), or the Graves (somepeople like them). I'm going back to tinkering on my old BMW. 35 year old Bing carbs are a lot easier to deal with.