Having had a Line 3, I would be interested also.
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I have never heard the stock Line 2 or Line 3, although I own both the Line 2 SE and Line 3 SE (both factory SE models). I am currently selling the Line 2 SE since I had a good opportunity to upgrade to the Line 3 SE, which offers slightly better bass response, although both are very good. Keep in mind the Line 2 standard version was a Class A recommended component by Stereophile.
Regarding the upgrades, when I researched this, it seems everyone thinks the SE versions are better than the stock versions by taking the units slightly off of dead neutral, and improving the midrange bloom, with other slight improvements in HF and other areas. I am very happy with both of my units in this regard. Chris Johnson with Partsconnexion, former president of SFI, told me he believes his SE "plus" upgrade improves on the factory SE upgrade by using better caps (he uses AudioNote Silver and the factory uses Multicap RTX) and by making improvements to the power supply, beyond what the factory does. I have not heard a Partsconnexion SE+ upgraded unit, but I am very satisfied with my Line 3 SE, and was also happy with the Line 2 SE, both of which were stock factory SE units. You may want to check with Anthem to see if they are still performing that upgrade, as I have heard they still service the unit. Also, if you already have good NOS tubes, be aware the upgrades may include tubes, so you should clarify. The factory upgrade included a new "special edition" faceplate. I believe the Partsconnexion pricing is higher for the upgrade, and the Factory SE units are more easily found used on A'gon. However, I also trust Chris Johnson and his opinion, as he has successfully helped me out with tubes and other stuff over the years. I wish I had heard both units and could help you out more. I too would be interested in hearing from someone who has done a direct comparison between the factory SE and Partsconnexion SE+ units.
The factory SE is definately better than the standard model, but the SE+ mod done by chris at partsconnexion is out of this worl. It brings the pre up to absolute reference quality. It will compete with ANYTHING on the market. This is my experience with the Line 3, 3 SE, and 3SE+. I never heard the Line 2 but i am told that others who modded their line 2s are just as satisfied as i am