You can still get the timing chain rattle with everything there and in good shape. One of my trucks has been doing it on start up for the past quarter million miles. Guides are stock oem pieces and in good shape.

The stock 22RE engine just isn't a powerhouse. Not even at sea level on a good day. Stock is something on par of just over a hundred ponies. You can modify them to do well, but stock, they're weak. Perhaps you've got unrealistic expectations for performance.

The white dots don't inherently signify anything that I can tell. I've seen them on brand new vehicles some times. I suspect it's part of an assembly line check-off procedure. And it's done occassionally by someone with a marker so they can be sure they've done it.

Cannot help you with the honk or the wire connector.