Hey Shrike
I'll try to help here.
First, for preload, the factory lists the full stoke of the fork at 5.1 inches. Measure this by putting the bike on the centre stand, unloading the front wheel completely, and then measure up the 5.1 and put a felt mark on the tube. Then you can measure down to this mark from the lower clamp to determine full stroke to your zip tie. Static sag should be in the range of 1/3 of stroke, or 1.6" +/-.
It sounds like your forks are not quite right, even with the Progressive Suspension springs. One thing I would be concerned about is whether your shop put the correct amount of fluid in the forks. On my 2G 600 forks, the call for LESS fluid in the forks with the Progressive springs than stock. If the shop did not remove fluid when they put in the springs, this could be part of the problem. Without enough air space, the forks will feel "harsh" on both small and large hits, and will NOT stroke completely.
You need to see if the fork oil level meets Progressive's recommended level. To measure fork oil level, you need to carefully remove the fork caps and springs, slowly compress the forks completely and measure the distance from the top of the fork caps to the level of the oil. Your Progressive Suspension instructions should list the correct level.
The only adjustment options you have are preload, fork oil level and fork oil viscosity, beyond changing springs (which you've already done). These are NOT the best forks in the world, but can be made to work reasonably well. For my setup, I have done the following, I'm 180 lbs and usually do longer tours:
1. Progressive Suspension fork springs.
2. Approx 1" preload (progressive recommends you start with springs flush with top cap. I have changed preload 3x until I got what I wanted - 1" over top of clamps).
3. 80% SAE 10W and 20% SAE 20W fork oil. So a blend to increase viscosity slightly. Firms up compression and rebound slightly, but be carefull, too much oil viscosity will make the forks harsh as well.
4. 1/4" higher fork oil level (slightly MORE oil) than recommended by Progressive. This makes the end for stroke stiffer, without having much effect in the early part of the stroke. Be carefull though, as mentioned above, too much oil will definately have a negative effect.
If I were to do it again, I think I would use Race Tech straight wound springs, although the Progressive DO provide a good compromise for touring.
Beyond these options, the next choice is to rebuild the forks using Race Tech Gold Valves.
I hope this helps...