You rely on instruments (microscopes and the like) to make better observations, good. You've also stated that we don't need to perceive things directly to know about them (like atoms) because we can see and predict the effects of things that elude our direct observation.
Now how far are you willing to go on that? For example is features 1, 2, and 3 are best explained by X, and X is best explained by Y, and Y is best explained by Z... How far could these chains of inferences go before they cease to be based on perception? Infinitely?
I also think you are setting yourself up to being forced to admit humans could possibly be omniscient if all knowledge can be gained by perception. A denial of this, forces you again to admit that there are things beyond perception, which is self-defeating to the hardline empiricist.
(Brownie points to the first person who can tell me which of Dewey’s critics first made criticisms such as these, although much more dense and sophisticated in jargon!)
There are also things that truly are beyond our perception. Optical illusions are perfect examples of this. Below is the classic Rabbit/Duck picture, you could never look at that picture and see both the duck and the rabbit; it has to be one or the other. This isn’t a cognitive error, but merely the limits on how our brain works.
