Myysterio
From trial and error on my part. I run the "outside the Tower part" totally on manual. Both traveling to, and then the looting part. I have turned the LUA back on, or started it up for the key combines. I have just found it to be easier to run it as a group that way.
As far as the pausing/unpausing thing goes, I have developed a routine I use. First I tell my tank (driver) to go get the mission (have my keys on the keychain) so he runs down all the stairs and to avoid the inevitable head bounce I switch over my veiw to another toon. Then I look for the mage to CoTH, both in the MQ2 chat window and by the casting of a spell. Then (and this is the key part) I put the Lua on PAUSE after the CoTH is complete, (the LUA not the toons) and let them do their buff thing (by taking the Boxr Pause off). This ensures that Boxr Pause is off BEFORE I go into the mission. Then I take the LAU Pause off and let them zone into the mission. Now just the way my PC works or whatever the reason, my driver usually zones in before the other 5, so the LUA is supposed to pause the LUA and it usually spits out a line about Not all characters are in the zone yet. Pausing. Or something similar to that. However on a couple of missions it does not do that so I manually pause the LUA to wait for the rest of the group to zone in, and then turn it back on (or unpause in this case). Now if you wait to long to unpause it can screw up the mission. And I haven't found a way to get it back on track so it can be completed. So I just zone back out (the group) and go to the next one, while cussing myself out for screwing it up. It's like anything else with this game and this software. Sometimes it works flawlessly and sometimes it doesn't. I try not to be too hard on myself, even though it's usually because of something I did wrong. But I have found that once you do do something enough times it does get better.
Anyways that is how I run Tower missions. Hopefully this helps or gives you ideas on how you should do it.
Vrak
edit: And just so you know, they are patching this as I type this reply out. (The Tower part)