"Did the Soul-Cost change on the lowest tier perks"
Yes, with the 2.0 update, one of the cost-configure options is 'half cost'. Because papayrus rounds down its decimals, this made perks that cost 1 Soul free. Because of this, the minimum was changed to 2 souls.

"This seems unfair" / "This seems like cheating"
Dragon Souls give the player power in the form of shouts. I simply extended the idea to include perks. I designed this mod to be able to progress with new characters from scratch as they develop. It also works with high level characters who have a storage of souls. I thought it was silly that once every 'word' is learned that Dragon Souls have no purpose. The cost is balanced in that low tier perks are cheap, and high tier perks are expensive. Also, it's up to the player to determine how they play...

"I don't like where the stones are"
I struggled with where to place these. In the end, I settled for somewhere that was open and obvious.
To comply with players who don't want to go through the main quest to reach them, they have been moved. A Map Marker is available North-East of Riverwood.

"Now I can't absorb Dragon Souls"
That has nothing to do with this mod. This mod does not alter how players interact with dragons.

"Why can't we just have perk points"
Now you can! The new system in V3.0 allows this, and makes it compatible with other perk mods.

"I don't see any stones"
Try moving this mod to the bottom of the load order. That tends to help most people. Also, be mindful if you have a mod that conflicts with the same area.