My guess is that you really don't have a suspension issue. What you likely have is a weight distribution issue. Does the TP replicator have multiple locations? If you move the TP too far back with a fully loaded 2up bike you'll get too much weight past the rear axle. Then you will "unload" the front suspension and get the kind of handling issues you're describing. Try moving the atP to a closer setting and I think you'll find the bike's handling will improve.
DoubleRunner; You may have a combination of issues, but the most dangerous is the weight distribution issue that
HeatWave spoke of earlier. I have had my '13 Anniversary CVO Screamin' Eagle Ultra since November 2012. Stock, I could run 100mph on freeways and hard through corners without any issues at all; 2up, solo, whatever. At about 4000 miles, I put the 'Adjustable TourPak Relocation Kit' on, loaded it with 500 pounds of people and probably 100 pounds of gear in the saddlebags, TourPak, & LuggageRack Bag. I checked the tire pressure, set the rear factory air shocks at 50 pounds, slid the TourPak back all the way and took off. This is about as hard as you can hit any motorcycle as far as screwing up the weight distribution, so I knew to be very wary of the changes while adjusting to the new setup.
Here's why I don't think this is the bulk of YOUR problem; I rode like this on my way to Canada up I-5 with the cruise control set at 85mph until I got in to Oregon. Heat, wind, wife swiveling every which-way to get pictures, and hands-free for a few miles while I got a picture of my odometer turning over to 5000 miles all without a wobble.
Here's what I would like to contribute to you and everyone who buys a TourPak relocation kit;
On my way down the other side of the Siskiyou Mountains on I-5 we came in to a fairly flat left turn on the freeway a bit too fast. There was a rough patch from about 25% to about 60% through the turn. My feet were on the highway pegs and hands on the grips. Decelerating into the corner while bringing my feet back to the floorboards for rear brakes, we hit the rough patch which bottomed the rear shocks out which made the bike push back toward vertical, send the weight to the front wheel which caused the handlebars to want to straighten the front wheel which caused me to try to hold everything upright while lightly braking as best I could and keeping my turn going. The weight behind the rear axle lightened up the front end significantly after each bottoming out of the rear shocks (did so 3 or 4 times, I wasn't counting!), and the braking action and the fact that we were going downhill and leaning in to a curve would bring the weight back forward again, all in rapid succession. This all added up to a death-wobble at, by then, about 60mph.
At this point, I would like to point out that this wasn't my first rodeo. I have been literally all over The USA West of the Mississippi and most of Western Canada on various motorcycles, the most recent 3 being a 1984 Softail, a 2003 Anniversary Road King, and my current 2013 Anniversary CVO Screamin' Eagle Ultra Classic. All-in-all some 40+ years of street riding, with the same woman on the back since 1984.
So, the death-wobble resulted in both of us having an adrenaline rush that lasted for a couple of hours and the TourPak being slid forward a couple of inches. No crash or damage to the Harley. I tested it out and was able to replicate the issue under controlled conditions, but the couple of inches forward seemed to bring it in to where it isn't dangerous under those conditions. Darn scary though!!
The moral is, as HeatWave said, "If you move the TP too far back with a fully loaded 2up bike you'll get too much weight past the rear axle." Be sure to test and redistribute as necessary before you go rockin' through the mountain curves!
The bottom line for you DoubleRunner is, I'm pretty sure you have something else wrong and I hope you find it and fix it before you mask it with something like a suspension change. Though I am going to change windshields too (6'5" and STILL don't like the taste of bugs!), I am positive that isn't your issue either. I would discount aerodynamics altogether in your case.
Good Luck!