1. do all your brushwork then make it a func_door or a plat - you can even go in and edit the brushes later in TB2 anyway. Not sure if clip brushes can be part of a func_door. Never tried that and not sure why you'd need to.
2. I don't think so but there may be some kind of hack I am unaware of. I know that ericw is actively working on his compile tools. There may be something there to query.
3. AD and Quoth have ways to spawn in monsters but this is for id1:
First make a room outside of your main map and place your monsters there. For each monster you place them in a trigger_teleport. I do mine like a little box intersecting their midsection. Make sure you leave some space (4 units minimum) between each monster and that the triggers never overlap. All of these triggers touching the monsters will have the SAME "targetname."
Now enter a unique "target" in each teleport_trigger.
Next you need teleport_destinations for each monster's trigger_teleport. In the "targetname" field of each destination enter the "target" from each unique trigger_teleport above.
Last you need a way to trigger the monster's trigger_teleport brushes. Let's just call it a trigger_once as your player enters a room. Remember above all the trigger_teleport brushes have the SAME targetname? Make that name your "target" in this trigger_once.
I know it sounds confusing but ask if I can clarify. It's harder to read than to do trust me. :) It's very easy to confuse target with targetname so just double check each step. And try to do one monster as a test first so you get the method down.
Also download the original map sources from id
here at Quaddicated. Load up a map you know well and then check out how id did it. E1M3 has the above "monster traps" method.