That's a consequence of using the drawing tools from the "wrong" style. Did you start this as a Mike Schley overland map in the first place?

See this FAQ entry for how to import the missing fills.

Are you talking about the Mountain Range tool or the Mountain Fill tool here? One is based on symbols, the other on a bitmap fill, so the procedure will be a bit different.

For symbol based tools, they adhere to the default symbol size you can get at by hitting the :CC2PRESETS: button. This must be done before using the tool.

For fill based tools, you need to change the scaling for that particular fill. You do that by clicking the fill style indicator on the status bar, going to the bitmap files tab, find the fill in the list, and then change the values for scaled. This can be done before or after drawing with the tool.

To comment on one other thing from your post

You can reorder entities using the ordering buttons, such as :CC2INFRONT:, :CC2FRONT:, :CC2BEHIND: and :CC2BACK:. All of these reorder entities within the same sheet. This does not fix the actual problem you were experiencing of course, but that has been discussed above, and this may help you arrange other things in the future.

That means you are picking the polygon in the wrong spot when you pick the polygon to trace. The spot you use to pick it is very important, as the trace line will always go through that point, so it needs to be on the section you intend to trace.

More here.

Re-scaling the entire map can be done simply by using non-visual scale and just selecting all the entities. Unfortunately, this doesn't change the scaling of the effects or the fills, which needs to be done through the respective dialogs.

I did write my own command that just does all of that for me.

There's more information in this blog article, especially in the "Rescaling Things" and "Rescaling the Entire Map" chapters near the bottom of the page.