Hello,
1) I suspect to two-lane edge that leaves the intersection towards the west narrows to 1 lane and vehicles already try to be on the correct continuation lane. To avoid this behavior, set the node type to 'zipper' where the two lanse merge.
You can diagnose strategic lane choice by right clicking a vehicle and selecting 'show best lanes'.
2) If you model pedestrians as vehicles then they will have an improper dynamics model (e.g. they will not use the whole width of the sidewalk for walking in both directions).
You can use od2trips with the option --persontrips to generate persons instead.
If you model pedestrian crossings as crossing objects you can also control them using their index link number. In the latest development version it is also possible to control both sides of the crossing with different indices (and of course you can chose indices freely) so you have the same power as with the current modeling approach.
Regarding placement, you can configure crossing shapes freely via xml input and netedit.
regards,
Jakob