Here is the layout to date

Signals

I assume those little black markings beside the tracks are supposed to represent signal locations?

The three around the end of the siding at extreme bottom are appropriately located for a CTC control point around the siding switch, but the ones in the middle make no logical sense. And if you're intending some sort of interlocking/control point in that area, you're missing signals on all the minor routes into the interlock. There's a huge difference between block signals and interlocking/CTC signals, but that middle area doesn't represent either.

Block signals are found at the boundaries of track blocks and only indicate occupancy (although reversed switches will also show the block as occupied). Block signals will therefore normally be paired, with one in each direction at the block boundary (I have seen rare examples of overlapped block boundaries in certain places.)

At an interlocking or control point, the normal indication of all signals is "Stop", and the dispatcher or tower operator can set a route and clear signals for a train. EVERY possible route into and through an interlocking must be protected.

Storage Yard, Layout "Plan"

What's the story behind the "storage area" to the bottom left? Appears to access the main via a spur (I assume that there are grades involved and it tunnels under the industrial area above? Have you calculated the elevations and distances and what the grades need to be to make that work?).

Does this represent staging for a branchline or other connecting railroad that has running rights into the yard for interchange? This could be the connecting track for your CP interchange, with a CP transfer that runs from active staging to the yard, sets off and picks up and runs back.

Is this layout meant to operate realistically, or just be a vehicle to watch trains run? That makes a huge difference on how to answer questions.