What revision fuel pump do you have? I am impressed that you are getting 120bar for the last 1,500rpm's. What's odd is that the program is asking for it, as you still have the stock pump, and i thought 110bar was the accepted limit. You deffently don't have a fuel pump problem.
Your AFR looks in line with you having a full exhaust. What are you seeing near redline, low 11 something? So, if the timing curve was a result of something the ecu was reacting to, i would expect to see a lower number (10.5-10.4 is stock).
ATDC means after-top-dead-center. Which is the negative number in the timing graph. It means that at the start of your timing run, the spark is not igniting till 12deg. after the piston has passed top dead center, on it's downstroke. Normaly the complete combustion process is done a few deg. ATDC, to push the piston down.
Dave may be on to something by asking your EGT's. It looks like GIAC is worried that the engine is going to get to hot. Which does not make sense, because you are not running alot of boost, looks like you can supply plenty of fuel, so if anything it could be much more aggressive all around. I know they use 2.5" exhuast and you have a 3", but that's no expanation for negative timing. By keeping that timing so low through the main boost time, it's keeping the cylinder temps. down, by not having complete combustion take place. If thats what there trying to do why not give a richer AFR and increase the timing map.
Personally it looks like your logs are correct. Apparently thats what GIAC designed. I had never heard that GIAC went with such a bizzare timing map, but dave has been around a lot longer than me and he mentioned it. And, your logs are showing it. If you call them and they confirm that is the program design, i would think about switching to another company. Not trying to pitch a product, but if you went apr, even stg.1 would give you more power than your tune now. Plus you have mods to go stg.2 way more power than it looks like your getting now.
Anyway good luck. I'll be interested in what happens. By the way, what's your gas mileage look like?