Jim,
Knocks and catches would not be "normal" in a well made model steam engine. A well made engine should have no discernable clearance in any bearing and be smooth and without tight spots throughout its rotation. A newly finished engine might very well have tight spots and assuming all else is in alignment there are ways to work the tightness out. For starters, on your engine, I would check the lateral alignment of the drive train. Disconnect the connecting rod ends and let them dangle from the beam and see if anything is visibly out of whack. Then try it the other way round, to see if for instance the crankpin end is a bit askew. That will dictate what next step might have to be taken.
Knocks would indicate two things, poor (loose) fit of journals or bearings, or drive train misalignment, or both, as gbritnell has so rightly suggested. In a beam engine the piston, piston rod, crosshead, connecting rod ends, beam, beam pin, crank rod ends, and crankshaft journal should all be in very close alignment with each other, within a few thou'. Sometimes when things aren't in line an end of the connecting rods will "pop" laterally as it attempts to seek its proper postion relative to the rest of the mechanism. One cause of this is misalignment of the connecting rod ends because they were drilled and reamed slightly askew resulting in the other end not lining up. Sometimes this movement is so subtle it can't be easily seen. Wallowing out the bearings to allow a misalignment is often the quick (but poor) fix.
If you Google "model beam engine" (or variations on that theme) you should find lots of examples of spiffed up beam engines (and some not so spiffed up), and many will be Stuarts. I tend to prefer a simple treatment myself, with a single-color paint scheme. Attached is a photo of a Stuart Beam I built a few years ago but which is no longer in my possession. The paint is 2-part hobby epoxy. The castings were first filled with casting filler and then primed, each rubbed down between coats, followed by two coats of color. The color is actually more a maroon than the red it appears to be. All of the machined surfaces are as-turned in the lathe, or as-finished with flat files; none of the surfaces were ground or polished. The Stuart Beam is not as easy a build as some (including Stuarts) would have you believe, it's a bit more than a beginner's engine, but it's a very good first
beam engine once you have something simpler under your belt.
