I believe that most of this can be handled with what the game has already: Perception. (Long)
Ambush: Opposed skill check of Ambush vs. Perception (-50 just like in making a combat perception). The Ambush skill check is done generally well in advance when the encounter is designed by the GM so the modifier is already in place by the time the PCs arrive. How long the ambushers took could give a bonus to his ambush check. Remember that the ambush skill gives a bonus to the damage equal to it's rank, so a highly skilled ambusher is doing quite a bit more damage. (Question about this: Are you all giving it as a number of Hits of damage, or as a modifer to the critical to increase that, or both? The last option would be really powerful.) The ambushee (did I just make up a new word?) makes thier perception check with all the same modifiers as a combat perception check. I would allow PC (and NPCs) to develop seperately a Sense Ambush skill if they liked, but it would be in the same skill category as ambush. Their resulting number on the Percentage column would be the amount of activity* they have after the ambush (100 max. except see below), with the -20 initiative still in place - unless they get a critical success/roll over which could lessen the -20 initiative by the amount of percentage over 100 they get. Yes, this could become a positive modifer, saying that they were just somehow able to respond instantly - perhaps with some sub-conscious advanced warning to even get a jump on the ambushers. Excellent rolls should be rewarded like excellent role-playing. Critical fumbles could result in entire rounds without reaction - the mage had his nose in the middle of a book while riding his horse, which reared and he then had to spend the time just staying on the horse (or not!). Some of the details should be described after the rolls and results as to explain them - and give humor.
Missed Teleport (& the like): Just make a perception/orientation roll with a modifier depending upon how different the situation is from what was expected. If you expected to end up on the path to the city, but landed in the river nearby instead, I would not feel wrong in giving at least a -50 to the roll. Use the percentage column just like in an ambush.
Do NOT let them take away your GM-given rights to decide what YOU feel is right and correct. A bunch of 3rd level character shouldn't/couldn't respond absolutely appropriately to every situation that comes up - so don't allow it.
*Alternatively you could just apply the difference between the resulting number and 100 as a negative modifer to anything/everything they do during the surprise round.