I tried reproducing issue 3 & 4. Couldn't get those to work. You should try removing the vc_traffic.asi and see if that happens. It fixed a few Missions bugs for me a while ago, with peds.
Removing vc_traffic.asi doesn't affect any of these bugs. Road switch is made in main.scm.
Update: Following completing Staunton, more notes that may be possible bugs:
1) Bridge between Fort Staunton and Torrington seems to have issues with car nodes too. Vehicles making U-turns etc.
2) On Gangcar Round-up I somehow saw a Purple Nine in Hepburn Heights: http://i.imgur.com/P03Tza9.jpg
3) During Gone Fishing target killed himself with a grenade. I heard it can happen in original game, but I've never experienced it and had an impression that it may be caused by frame limiter turned off. Additionally, fish cutscene took place underwater.
4) At the end of A Drop in the Ocean as I skipped cutscene as soon as possible, fade screen was interrupted by blinking black rectangle (corresponding to widescreen view).
Update 2: As I completed 100% (157/158), I added some more stuff I noticed.
5) Bike mission on Staunton Island seems to be supposed to take place after Grand Theft Aero, but is always unlocked. Timing is not too tight to complete it without using a hole in the wall, so that's not a serious issue.
6) For some reason coronas in the bike mission on SSV occasionally didn't render. There were blips on radar though: http://i.imgur.com/BNP71sc.png
7) Timer on S.A.M. was slightly off for me, it reached zero before plane reached runway. In original game timer is slightly off too but that's no more than by a second or two.
8) Making colombians follow player during Bait is very hard, but that's noted in 'Mission coding' topic and requires rewriting pathfinding to treadables-based to at least get it to III level, where it was far from perfect too.
9) On Vigilante suspects occasionally tried to leave SSV which resulted in stuff like this: http://i.imgur.com/it6xXyU.jpg
10) On the bridge between SI and SSV abandoned vehicles weren't updated properly, which didn't happen in III: http://i.imgur.com/it6xXyU.jpg
I think there is a function CCarCtrl::MapCouldMoveInThisArea with hardcoded bridge coordinate that added checks for abandoned and wrecked vehicles, which even remained in VC with same coordinates. Maybe fixing hardcoded coordinates in this function can prevent this from happening.