The savegame:
http://www71.zippyshare.com/v/kiUN0PKT/file.html
1) In-transit cargo is still off (that might be related to the 8.5 billion cow bug I posted yesterday). In this case, it's the bakery in Arlsing that reports 14 flour in-transit, but which are nowhere to be found.
2) I tried to sell/retire the convoy (no. 108) that's going to the bakery: "Depot found but could not be inserted in schedule. This is a bug!". I thought that would fix the transit numbers, but it doesn't.
.... wait: selling/retiring only fails while the game is paused.
3) In some places I can't build bridges: "Bridge blocked by way above or below".
4) The range feature has some problems: I tried to start a new line connecting several villages, but when I tried to send the first convoy it said something about exceeding the 30km horse range by 3km. But I can add stops before the one that's causing the problem, send the convoys on their way and then delete these stops later, with no range warning.
One more oddity: this textile mill has 82 textiles and 109 wool in storage, and has had roughly the same amounts for ages. But storage numbers are zero, except for a brief surge to 1.
I should be very grateful if you could report only one bug per thread as set out in the bug report guidelines (http://forum.simutrans.com/index.php?topic=13026.0), as it is extremely difficult to keep a track of what has been fixed and what is still outstanding if there are multiple bug reports per thread.
I have fixed some problems with the in transit numbers recently - can you check whether this addresses the issues that you have reported?
I am afraid that your saved game file has now expired, so I cannot investigate issue no. 2. No. 3 does not seem to be a bug, as that error message does not by itself indicate a bug. As to no. 4, although you can delete the stops, when the convoy actually gets to make the journey that is too long, it will refuse to start out on the basis that it is out of range.
If you can re-post the file so that I can look into issue no. 2, I should be grateful. As I wrote originally, however, since I do this as a hobby and have very limited time for this, it would be much easier if you were to post one bug report per thread.