Try an initial setup of 1" drop per foot of sluice, and level from side to side.  In your case, about 4 inches of drop.  If you meant you are feeding 2 shovel fulls from a #2 shovel at a time, you are definitly overloading the feed rate.  You can adjust you angle and flow rate from there.

With normal flow rate of water, it should clear out in less than a minute when you feed in a couple garden trowels of material.  I like to classify to 1/4 inch before running through my sluice, but it is a 30 inch backpack Royal.

The crossbars you refer to are the riffles.

If you need to rake out bigger rocks, you can do it, just run you fingers the direction of water flow when raking them out, trying to make minimal disturbance of other material in the box.

To help in initial setup, I set my boxes on the floor at a 1" per foot drop and stick on the self adhesive camper levels so they show level with that amount of drop on the box.  Makes setup in the creek a little faster.

When you submerge the end of your box, you will lose water velocity, as the water now has an escape other than going through the box.  You will notice material build up at the area that is under water in the box as not enough flow exists to clear it on out.

  If your stream is that small, you may be able to get enough water flow through that big of a sluice as well.  Can be tough to fit that big and wide a box on a small stream, and still get the setup needed.   If you have access to a smaller box, or something like a LeTrap, that would likely be a better setup for a small stream like that.