Actually it really doesn't matter much whether the channels are vertical or not or even if they are even! Some people demand 1" squares while others demand 1/2" squares or the lap is no good. The truth of the matter is that it really doesn't matter how big things are just so long as there is some. If you want to do 3 directions for the channels (at about 120deg. for example) then be happy and do it that way. The lap will work just fine!
As to the channels in the tool, if you don't care about the pitch going in there thus using more pitch, don't worry about that either.
The only important things about a pitch lap are that it's mated to the mirror well and does have some channels. You can even do microchannels with some wedding veil stuff to onion bag material or whatever you might have.
A lot of people agonize over the "quality" of their lap and as far as I am concerned, it's all a big waste of time. Just make sure that the pitch is mated over the surface of the mirror (no pads that aren't in contact and not center area or edge area that isn't making good contact) and the lap will do a good job.
Also, don't worry about "bubbles" in the pads as those end up just being more channel area and won't hurt anything.
As to temp, you don't want it too hot as the pitch will move quickly then and you won't be able to make any form with it at that point. After it cools down a bit then you can start making it stay where you put it. After you have played with it for a lap you will understand what that means.