I want to add a few more comments related with speed limits fixing.
1) It would be great to have real world information as for the last few years available in the Internet, about the tracks speeds for NS and NJT. There is such information available for Union Pacific divisions in the west.
2) When working on fixing track speeds it is better doing that with a short train than an single engine, at least of 15 to 20 cars (or 10-12 cars if passenger).
3) Remember that QD considers the trains as high priority and therefore you will see the passenger (or primary) track speeds. You need to work in the editor when looking at freight speeds. And yes you have to fix both speed limits,
4) Looking at your first screenshot (2 posts before this one) you can read 4 changes in speeds in the HUD: 50-60-40-60 in a very short stretch (about a mile). While that may be true in the real world, it is not logical, increasing the speed to 60 (?) to reduce it again a quarter of mile after. It could be more logical if it were 50-40-60, indicating a reduction of speed that may be required because of a bridge, a track issue, etc... You have to fix also that kind of problems. The best is having real tracks information.
5) There is no other way to fix track speeds other than using the SHIFT tool to visualize the speeds on track, followed by the usage of the selector to change the wrong speeds and editing the values in the inset.
6) Be aware that you can have very short joints (an inch or even less). Those are bad joints over the design speed track. They will be in some cases, very difficult to fix with the previous solution with the presence of two or three speed changes. You have to overlap using the selector over the three (two) speeds.
7) If I were you I would remove all speed changes in all signals. They can´t be seen in TS HUD. Where they are used (Sherman Hill), they need a set of rules. However if you do not have a divergent track, placing a speed change in a block signal has no sense at all.
8) You invite to get help from others. Speed fixes are quite difficult to describe and you don´t know what the author wants or is following. The best is lending the track to someone so he fixes if not all , a lot of the speed fixes but always in the same area.
But this is quite time consuming, though you have places with less issues as in Hoboken (but there are some).
9) You are lost? I don´t think so. Follow what I have written and you will get it done soon. You can do it. It is only time consuming. Every time you save you get a new tracks.bin. You may want however hold the Workshop updates a little bit. Start from south or from north and always follow the line to the other side, advancing a little bit every day.
Take a look to this thread I wrote a few months ago:
viewtopic.php?f=7&t=16256&hilit=+speed+limitsI won´t be much available in the next coming days (not sure how long).
Good Luck
