New Timer Window:
Let me start with a big...
*THUMBS UP!!!*
The ability to time AE's accurately so a raid force can joust is essential to high-end raiding. Using 3rd party programs that you have to click (and those take focus away from the EQ2 window) either causes the AE times to be off or the person doing the timing to not be able to play their class to its fullest. The same goes for using real life stopwatches etc! I can't tell you how excited I was to see a full functional in game count down timer and as a bonus it does multiple count downs (SoE loves to add more and more AE's to mobs to make them more difficult.)
A couple of questions and requests:
Default Times: Can you tell me where in the eq2_mainhud_timer file that the default times for the 4 timers are located. I would like to modify them to the 4 times I use most often.
If you know how to use the ui builder program, that is probably the best way to modify the default times. It's kinda hard to explain exactly why, but... for the short version: Even though the timers look like progress bars, they're not. They're colored rectangles that start out way to the left of the timer window and move steadily to the right and do not appear until they move into a visible rectangle. How far to the left they start determines how long they take to finish up filling the rectangle. So, to change the times you have to do math on all 18 of the rectangles (in each timer) to determine their starting positions.
If you load the window in UIBuilder, you can set the times by toggling the visible property on the minutes and seconds you want and a macro that's in there will auto-calculate the proper positions. Then you can save the changes and use the modified file.
Wow, that sounds complicated. Maybe I'll take a look at making an easier way to change the defaults. 
Options/Interface Window: Would it be at all possible to create an options/interface window for the Timer. So someone could simply click on whatever small button you could add to the window and it would bring up another window. In this window it would have spots to enter the 4 different times one wanted, as well as an area for options (see later requests/ideas)
An options window is doable. This was an initial release, so I went for simple to see if anyone was really interested in it, or if it was just a couple posts and nothing more.
Final 5 Secs Variable: When the timer hits 5 seconds it switches to the "faster" red count down bar. It would be very helpfull if we could select 5/10/15 seconds for this function.
Possibly doable, but I'll have to think about how best to tackle. Because of the moving rectangle thing above and the fact that the speeds have to be an integer number of pixels per second, there's limits on what times work properly. That is incidentally why the window is not resizable. The visible bar must be a multiple of 150 pixels wide for the green bar to work (it counts from 3 minutes to 30 seconds (150 seconds) and moves at 1 pixel per second.)
* Many times depending on the size of the AE its important to call the "Joust Out!" at 10 seconds or sometimes even 15 seconds if the melee has a long way to run in order to get out of the AE, or for instance when there is an incoming memblur and the tank needs more time to get longer casting skills skills up.... etc!
Sound!: If a generic windows beep (or even a customizable wav, set in the atually xml file) could be played when the timer hits the final 5/10/15 second mark!
A sound is definitely doable. I've tried it in the past in one of my other mods successfully. Only caveat is that it has to be one of like 20 sounds already used in the eq2client, like the new mail notification or the tradeskill first time pristine chime.
* This would help facilitate someone fully being able to play their class role on the raid and still being able to time the AE. They hear the BEEP! and boom they are on their macro telling the raid force the the AE is Inc!
Auto Repeat/Loop: An option to have the timer repeat/loop automatically. So take a 30second timer, it would hit the variable 5/10/15, it would beep, it would hit 0 and it would automatically start counting down again!
Repeat is not doable. The client does not like timers starting other timers. Most likely because of how convenient it would make it to write bots. The end result is that trying results in a crash to desktop.
(Even though it looks like the red timer starts after the yellow timer finishes, in reality what happens is the red timer starts at exactly the same time as the yellow one, It's just so far to the left that it doesn't hit the visible window until just as the yellow timer is finishing.)
The ability to finally have a piece of the game timing AEs is awesome! To be able to start and stop it from the same Hotbar that I cast spells from is invaluable! The above just being suggestions for milking everything possible out of the new feature!
Thanks and let me know if there is anything I can do to assist.....(edited) if you have the time and if any of the above is possible