I don't know the L28s very well but your timing should keep going after 3000 RPM, all the way up to redline. Now, 39 degrees seems like a lot at 3000 RPM (assuming 100% load, 101 kPa), especially with such high IAT readings. If that's really what the engine likes then there's no much you can do, but on my VG30ET I have 15 degrees at idle and it ramps up to 45 degrees at 6500 RPM. I am around 30 degrees or so at 3000 RPM. This is at 100% load, in boost I do remove timing but the trend remains.
I'd add that intercooler in first, before worrying about boost threshold, that will help alot. I see 16psi at 3000 RPM.