Let me start by saying that the native Insteon support in the Vera is not very good. (If you search the forum for Insteon, you will find many tales of disappointment, which is why I wrote my own Insteon implementation that I use with the Vera.)
I have the Garage door kit you referenced. I am not sure it will do everything you want, but it can probably get you pretty close.
If devices are timing out, then you may have a problem with either the PLM and the IOLinc being on different phases, being too far away, or having a really noisy power line. If you read through some of this thread http://forum.micasaverde.com/index.php/topic,8910.15.html I went in to some detail in a few posts about how to troubleshoot Insteon devices. If the power line is noisy, you can buy a filter from Smarthome that you can plug the device generating the noise in to. However, I would check phases and distances first.
Assuming that you can move the pieces around, a good way to verify that it will do what you want is to plug the PLM directly in to the power outlet on the front of the IOLinc. Insteon commands will flow through those outlets with no problems. This will rid you of pretty much any problem except noise. It is a good way to remove a lot of the variables for initial testing.
As far as using the sensor to detect the up/down state of the door, it is pretty easy. The instructions that came with the garage door kit should help you get the wires connected properly. Then, you just need to attach the sensor to the garage door. I “cheated” a bit on mine and used some liquid nails to secure the sensor to the concrete, and also to secure the magnet to the door. It has been working fine for about the last year and half through nasty Utah hot summers and freezing cold winters. The sensor has also been run over by the car a couple of times with no problem.
If you want to be able to detect when the door is closed, and when it is fully open, you will need two sensors. One for fully closed, one for fully open.
As far as your scenes go, I am not sure I understand exactly what you are trying to do. So let me take a stab at it.
Scene 1. - I am not sure how you would “show the motor on at 6am and off at 6pm”. If you want to open the door at 6am and close it at 6pm, that is easy enough. The control wires on the IOLinc need to tie in to the terminal on the opener and then the IOLinc needs to be set in the right mode to control the opener. (Usually ‘momentary C’.)
If, on the other hand, you want to actually control the power to the opener, so that it will only allow opening and closing from 6am to 6pm, you will need something like an appliance linc or outlet linc. Then you would just set up a scene to turn the power on a 6am, and another scene that turns it off at 6pm.
Scene 2. - There isn’t any way that I know of to actually turn the sensor off. The Vera has an “Armed” and “Disarmed” state, but those states don’t actually do anything to the IOLinc. It is just an internal flag that you can use to allow the sensor to be bypassed. So, if you use the sensor to trigger something, you have to make sure you use the option to trigger when something happens and the device is armed. Otherwise, it will trigger any time something happens. Since the primary use of my IOLinc is to read the door state, I don’t bother with the Armed/disarmed states, I just want to know if it is open or closed.
Hope this helps a bit!