Speaking in terms of pure speculation I am going to say that your problem most likely isn't related to the noise you are hearing regardless of the source. This is based on your experiences with timing changes etc. It sounds to me like you are on the right track with tuning and lowering coolant temps etc. Just my 2 cents on the noise, if the trans does have a 2nd gear specific noise then it would probably be in the rear planet and/or captured bearing as well as sunshell flex. I understand your desire to upgrade to a 4L80E, but just remember that they are heavier, take more power to operate, and are relatively more expensive generally speaking. They also have their inherent flaws to deal with. If you can build a trans then I'd say build a solid 4L60E instead. You can throw upgrades that basically just increase pressures and clamping forces at the trans all day long. But, if you don't actually upgrade the internals and have stock frictions that have seen slippage and been abused, then nothing is going to improve the function of the trans and you might actually be worsening the problem.