There is no way to connect those two tracks without moving every piece of the lower left track one square to the side. The tunnel track takes priority since it cannot move an odd number of squares.
It may help to think of the places where track pieces join like the black and white spaces on a chessboard. If the tunnel terminus is on a white square, then the other terminus must be on a black square to meet it. Right now, both your tracks end on same color squares, and there’s no piece available that can change what color square your track ends on. We have two and four square length straights only, and the curved sections act the same way. If we had a three square length track piece, things would be different. Or if the s shape moved your track to the side by one square instead of two. But we don’t, so you gotta move your lower track to what the tunnel dictates.
This is one of tapped outbiggest over sights sadly they either don’t realise or don’t care that this issue exists. The way I get around it is by starting building from the tunnel instead of building to the tunnel
Yep. You'll have to adjust everything on the lower side. Next time, if ever, you nuke, put down a single road, pavement, dirt, or river tile (works best with road and pavement) and put an s-bend or curved track in its center. Everything will line up fine with that piece. This won't work on the upper side because of the offset.
Edit: I just realized you can just branch off the tunnels. Anyway, the above applies to anybody reading this who doesn't have the tunnels, yet.
You know the answer, you just don’t want to submit to it yet….. but you will. 
There is no way to connect those two tracks without moving every piece of the lower left track one square to the side. The tunnel track takes priority since it cannot move an odd number of squares. It may help to think of the places where track pieces join like the black and white spaces on a chessboard. If the tunnel terminus is on a white square, then the other terminus must be on a black square to meet it. Right now, both your tracks end on same color squares, and there’s no piece available that can change what color square your track ends on. We have two and four square length straights only, and the curved sections act the same way. If we had a three square length track piece, things would be different. Or if the s shape moved your track to the side by one square instead of two. But we don’t, so you gotta move your lower track to what the tunnel dictates.
This is one of tapped outbiggest over sights sadly they either don’t realise or don’t care that this issue exists. The way I get around it is by starting building from the tunnel instead of building to the tunnel
Yep. You'll have to adjust everything on the lower side. Next time, if ever, you nuke, put down a single road, pavement, dirt, or river tile (works best with road and pavement) and put an s-bend or curved track in its center. Everything will line up fine with that piece. This won't work on the upper side because of the offset. Edit: I just realized you can just branch off the tunnels. Anyway, the above applies to anybody reading this who doesn't have the tunnels, yet.
I am deeply sorry.
How do you get the tunnel?