The MapSource user interface is clunky, to be polite. It does function well after you get used to it.
You were almost there. When you copied and pasted the waypoints, you transferred them as an unordered collection of waypoints. You need to use the Route Properties window, which presents the waypoints in sequence as a route. Here's how, in more detail than you probably need. It is faster to do than to read:
1. Start two instances of MapSource and arrange their windows so you can see both at once. In one, which I will call Left, we will open the routes as ACA publishes them. In the other, which I will call Right, we will build combined routes. Since you are riding westbound, we will start with the easternmost routes.
2. Open TA12v007.gpx in Left. File > Open.
3. Open a new Mapsource file in Right. File > New.
4. Optional. Do this if you want to combine the points of interest (POI) waypoints as well as the route waypoints.
In Left, click any waypoint in the Waypoints tab in the left pane. Ctrl+A selects them all. Ctrl+C copies them to the clipboard.
In Right, click anywhere in the waypoints tab in the left pane. Ctrl+V pastes the waypoints there.
5. In Right, start a new route. Ctrl+R. A Route Properties windows opens.
6. In Left, double-click on the last route in the Routes tab.
7. Its Route Properties window opens. Ctrl+A selects all the waypoints (via points) in the route. Ctrl+C copies them to the clipboard.
8. In Right, click on the top-most waypoint, if any. Ctrl+V pastes the copied waypoints above the one you just clicked.
9. In left, close the Route Properties window.
10. If you wish to combine more routes, on the Routes tab, double-click the next route to be combined and go to Step 7. Otherwise, go to Step 11.
11. In Right, uncheck Autoname. Enter a new name for the combine route. Click OK.
12. If you wish to make more combined routes, go to Step 5. Otherwise, go to Step 13.
13. Save the file containing combined routes. File > Save As. Navigate to the folder where you wish to save it. Enter a file name. From the drop list in Save as Type: select GPS eXchange Format (*.gpx). Click Save.