I cannot tell which need to be separate power districts from the layout photos.
If you want to keep the two on separate transformers or throttle handles at the cross, cut where you see the lines with x and solder a jumper wire across.
Then, a dead spot on the straight will be eliminated and the two line will cross physically, but be separated electrically. If you are isolating the line at the switch turnout from the thru, it should work ok.
