When retooling The Scouring of Gate Pass for my customized Pathfinder-based conversion, I noticed that the treasure range was skewed, both high and low. In game play through the first half of the adventure, the player's choices skewed it low. For example, by choosing to treat the Shahahlesti agents (generally) as rivals to be outdone, but not enemies to be defeated and looted, they passed on a range of rewards. In addition, when dealing with some of the Black Horse mercenaries, they have felt more pressed for time, so they did not loot to the bare bones all their foes equipment, but just what they could readily gather. For example, they left the armor for the vast majorities of their foes behind rather than haul it around in the middle of the night hoping to find someone to sell it to before they started their 300 mile cross country trek.
I chose to compensate some by having the party's patrons in the Resistance provide them more than just instructions. When they stayed at the church of the Aquiline Cross, they were provided some gear to help them, including potions and healing kits. Depending on how your party works through events, you could include some extra rewards scaled up by and down by what you needed to keep your group at the appropriate level for your campaign.
The value of the trillith boons that can be gathered do really skew things from a "wealth by level" calculation, and more than just what they do to total wealth levels. The value of the boons generally jump your character's over the guidelines for their levels for a while. However, the boons are a double edge sword in this respect. While very powerful, they are also not suited to individual characters. By that, I mean that the d20 rules in general assume a combination of a stacking boost to a character's primary role and a distribution of defenses to shore up the character's weaknesses. As an example, a simple +1 magic weapon runs 2,000 gp. The first +2 attribute boosting items run 4,000 gp. The party that ends up with a +1 dagger in the hands of the wizard and a +2 Headband of Intellect on the fighter is not nearly as effective as the one where the wizard has the +2 Headband of Intellect and the fighter the +1 battleaxe, even though numerically these are about the same value.
The Boons let the party do amazing and interesting things, and really add to the story. I love them. But they do not specifically boost any character's profile, so calculating their relative value for effectiveness gets tough, in my opinion.
I am afraid that the work I am doing for adapting and converting the material will not directly help you. For one, I'm specifically reworking the gear to take advantage of the wide range of choices that are now available under the PFSRD than were available for the d20 SRD rules set. In the process, I am also specifically going for some gear that works for my party or makes them make interesting choices. For another, I am planning on having a few original scaling items using the Pathfinder Unchained guidelines. While the Living Blade of the First Tree makes an obvious conversion as a Wonder that way (and surprisingly easy to do), I am also going to have the Soul Shroud be a scaling item, as I think it too interesting in flavor to let it be discarded in the game.
Depending on where you are at, there are some points where different factions or group would have reason to reward or equip the party, and you can use those moments to re-balance the groups wealth and equipment through the campaign. While I mentioned one point in the first adventure, you could also have Councilman Menash do more in the first adventure. The ending points for the 2nd, 3rd, and 4th adventures puts the party at a point where they could receive patronage, boons, or sponsorship in the context of the story. You could even opt to have the Lyceum "issue" equipment for a mission, especially consumable gear, and then have it be reclaimed for other efforts in the war if unused, allowing you to boost or scale back some gear as you need.