Personally, I think HP Quints, AD marks, armor seals and MR glyphs work the best as runes. Why take HP? Thresh's early game stats have been nerfed so severely, that he's way too squishy for other aggressive early game supports and ADCs if left with mere 550 hitpoints at level 1. If you don't take any AD/penetration you lose lot of that early fear that Thresh has to pose for´your enemies. On the other hand, if you take only AD without Health, they'll notice that they can hit back just as hard. I think OTG has counted which marks would be most beneficial for Thresh early-mid game.

Currently, Thresh has 2 noticeable flaws that are rather easily exploited: low base stats and lack of mobility. So IMO, the best way to build your runes and masteries, is to both reinforce the strenghts, but also recover the weaknesses.

Key points:

• Thresh is ranged, and can choose to stay at range or go melee
• Thresh has no escape tools of his own
• Thresh's early game damage is largely based on his empowered auto-attacks

So, my masteries are 0/9/21, as recommended by Gleerglarbu, to attain
- higher movement speed and mobility to keep yourself alive
- CDR and other important base support stats
- tankiness

Otherwise, 9/21/0 and 0/21/9 are also possiblities, but I found myself liking the more utility focused tree the most on Thresh. But as they say, whatever works for oneself.

Can't really comment on maxing W first, because I usually take points in E and W according to how my lane is going. I can however say, that the shield scales lot better with souls than skill points. Other than that, I have to say that I admire the effort you have taken in building this guide. However, I would like to see some more coding.

You can land an auto between Death Sentence-pull and Flay, allowing a bit more damage (unless you know that the enemy has some form of extremely quick dash). Flay reset your auto-attack timer.