Bart,
The dowel is 1 1/4 diameter, not long, and the diameter is not critical, nor is the length - provided it is high enough to support the wedges. That just happened to be what I had around - part of a clothes pole from a closet. The main thing is that I feel it needs to be round to allow the wedges to self align when pressuring the end beams to the ends of the sills.
The ‘spacers’ as you refer to them are assembly wedges. Once the parts are placed in the fixture (side sill and intermediate sill), put a small amount of pressure on the end beams and then wedge the side and intermediate sill with the wedges. This holds everything tight and square. Look back at my September 6 post above and in the lower right hand corner of the second picture there are six pairs of wedges (3 horizontal and 3 vertical on top). If you look close you can see the angled cut in a couple of them. I could have shown them better. I will post a pic or two tomorrow evening, too late tonight to break out the camera.
If you would like, I can make a set of wedges for you for the fixture. They are the only part that is not simple square cuts. I have a tool I picked up in a garage sale I set up for the angled cut in the wedges.
For your reference I make a quick drawing of the wedges I made for my use.
http://www.gscalejunkie.com/GeneralPics/6000Flat/Wedges.pdf
The .125 dimension is the saw kerf on my thin kerf blade on my table saw.
I will also post a pic of two of the four frames I have going now.
Bob C.