Yeah, equipment goes up to +9 and you can get up to 10 of any rune once...
Being able to stack 2-3 level 3 set affinities really breaks the scaling. Also, after the first 10 NGs, you only have to add one new burden per NG, rather than two, and at NG20, you do not add any new burdens, so my guess is you really start to outscale the game without adding some house rules.
I think the ideal builds are these:
Tank: Obsidian Weapon/Chest +9 (for +30 vitality AND +20% vitality), Kin Helm/Cape +9 (high stats, plus return damage and a free revive), plus Ammonite Trinket +9 (for +30 & +20% armor).
Strength: Drowned Weapon/Chest +9 (+30 & +20% strength), Kin/Helm Cape +9, plus Warden Trinket +9 (+30 Dex & +20% crit chance).
Magic: Leviathan Weapon/Helm +9 (+20% Siphon, +5 Soulsteal runes), Crescent Chest/Cape +9 (+30 & +20% Intelligence), and Scholar Trinket +9 (+30 Focus & +20% Magic Crit Chance).
You can also get up to 50 points in each of Unbreakable Will etc. to raise the manor level caps, raise each characters level to a cap of 50, and get the Charon affinity up to level 100.
I have seen it estimated that it will take around NG+73 to fully max out everything in the Soul Shop, with all gold scar challenges.
Two hints that are not completely obvious:
1) Always talk to each NPC. They will all give you 500 souls eventually when you finish their dialogue tree, including the safe, the strike dummy etc. This even goes for the Pishon Dry Lake dragon. The easiest thing to do is to lock the dungeon after you defeat Tubal, go talk to the dragon and retire hero. Rinse and repeat until five new heroes have spoken with him, and he will give 500 souls too.
2) Once your manor is pretty well leveled, giving gold to Charon can actually be a good use of gold. Every Charon level is worth +1 to strength, dex, vitality, intelligence, and focus and +2 to rune weight and equipment weight. I once accidentally donated 1.8 million gold to Charon around NG+2 after a nearly full castle clear and flipped out. Then I realized I had raised each stat like +12 and my rune and equip weights +24, and I think it was actually the most efficient use of my gold at the time, lol, since I had so tediously avoided donating much excess gold.