How can you tell if a scratchbuilt part is within the scale of the model you are building? For example, let's say you are making bins with open covers for your tank. How do you know if the thickness of the sides and cover are correct?

Since these would be unarmored sheet metal, almost anything is going to out of scale. Thin brass would be the closest butvery thin plastic, say .02 inch would come close but may be too thin to get an adequate bonding surface. If it's going to be in a closed position, use .1 plastic for the sides and .02 for the top.

OK..... 16 guage sheetmetal is .059" thick or .00168" in 1/35 scale yep..... kinda thin................. Ya just kinda adjust........ it's not going to be "perfect"

As a practical matter, plastic thinner than .010" is not stiff enough to represent a freestanding piece of sheet metal (though it can be glued onto the face of another part to represent a closed access panel or something). That said, the average viewer cannot distinguish much, if any, difference between .005" and .010" thickness, so I just use ten thousandths styrene to represent sheet metal. For large spans, even .010" is not stiff enough, though, and .015" must be substituted to eliminate bowing.
Thin brass or aluminum is a possible substitute, and Aber among others make large photoetch sets for thin section armor panels and sheet metal stowage boxes.
However, making your own part from sheet metal stock is dodgier, as it is difficult to cut the material with tin snips without imparting any curve to it.

Thin sheet metal can be cut flat by repetitively scoring with
a sharp blade, scalpel or similar. Don't use force.
If the sheet metal is aluminium (aluminum) or brass the
hardened steel of the blade will have no problems cutting
through.
Use a sheet of glass or a flat steel plate as cutting surface.
The cut will start to go through in small spots, this is why it
is important not to use force since the first holes could cause
the blade to snag at the thin sheet metal and pull it away or
give an unclean cut.
The edge of the cut will need some finishing afterwards,
lay on flat surface and use a very fine file or fine "sandpaper".
/ Robin