Finn, very confusing problem.

Let's start by getting the nomenclature that we use in agreement.  This is an exploded view of the clutch assembly.  Use the nomenclature provided in this illustration.  Although the illustration is for an LS clutch, the DR clutch should use the same nomenclature.

You should not need an extra Washer (7).  There are two thrust washers in the assembly (2 & 7).  They are both 2mm thick.  

Washer (2) is 44 mm O.D.  It goes in between the Spacer (3) and the transmission bearing.

Washer (7) is 40 mm O.D. and it goes between the Sleeve Hub (4) and Spacer (3).  It is nested inside the Primary Driven Gear (1).

I suggest you assemble your clutch on the input shaft and leave out the clutch plates.  So, install the Washer (2), Spacer (3), Primary Driven Gear (1) with Oil Pump Drive Gear (17) and Roller (18), Washer (7), Sleeve Hub (4) with Pressure Disk (13).  Install Nut (5) and lightly tighten.

You will essentially have the clutch assembled on the input shaft but there won't be any clutch plates.

Verify that the input shaft will rotate independently of the Primary Driven Gear (1).

Verify that the Primary Driven Gear (1) is free to rotate within the backlash limits of the Primary Drive.  The Primary Driven Gear should be free to rotate slightly and wiggle a bit.  It should have about .010" axial movement on Spacer (3).

Verify that the Pressure Disk (13) is free to move in & out and that it engages with the splines on the Sleeve Hub (4).

Verify that the Oil Pump Drive Gear (17) is free to rotate slightly on the Primary Driven Gear (1).  It should not be pinched between Washer (2) and the Primary Driven Gear (1).  It should move in & out slightly, and be free to rotate within the limits of the drive pin (Roller 18) and slot in the gear.

Take a bunch of pictures and let us know what you find.

If you have difficulty rotating the Primary Driven Gear, make sure that your Oil Pump Drive Gear (17) is oriented correctly.  I know you have made a set of high-speed oil pump gears.  Make sure that the drive gear isn't too thick and that it isn't turned around.  Make sure that some feature on your gear (like the small screws used to fasten the gear tire onto the new hub) isn't interfering with the Primary Driven Gear (1).  As previously mentioned, the oil pump drive gear should be free to rotate slightly on the Primary Driven Gear (1).  It should rotate within the limits of the drive pin and move in & out slightly.

None of these screws should hit anything.

DragBikeMike sure is thorough!

My clutch assembled properly with the DR650 parts inserted - no additional washer was needed.  Something you did isn't proper.

Although the early model primary driven gear (1) looks pretty much the same as the late model, I did note a few differences.

The early model has these unique semi-circle stops cast into the bottom of each slot.  Looks to me like these are intended to act as stops for the tangs on the innermost drive plate (8).  I believe they are incorporated to prevent the tang from binding in the radii at the bottom of the slot.

I assembled a clutch using the early model primary driven gear (1), the modified (bored out) LS pressure disk (13), and the DR650 sleeve hub (4).  I installed six drive plates (8), one drive plate (9), and six driven plates (12).  I used the stock thrust washers (2 & 7).  

I left out the wave washer assembly (10 & 11) because it is very hard to compress and will interfere with travel checks on the pressure disk.  To get accurate travel readings you must start with all the plates in intimate contact.

To permit checking travel, I assembled the clutch with two light checking springs.  These light springs will bring all the components together while still allowing me to cycle the pressure disk with my fingers.  The light checking spring is on the left, stock spring is on the right.

This is the special sleeve installed on the pressure disk.

Since the clutch release mechanism travel is .065" to .070", the pressure disk will hit the hard stops before the clutch hand lever has moved through its full range of motion.  Something will eventually break.

Adding another washer (7) might fix the travel problem, but it moves the rotating release plate (14) too close to the release arm (24) in the clutch cover.  IMO, this is a bad idea.