They probably could, but I'd like to think that all of that code is almost entirely useless without the help documentation and the plugin parameters from the paid ones. And frankly, if someone could successfully build a system from only the core plugin that worked, that guy probably could've made his own system from scratch, and it probably would've been better than mine anyway.
Okay fixed it:
Literally just added + this.helpAreaHeight() to line 1868:
var wy = (Utils.RPGMAKER_NAME == "MV") ? this._helpWindow.height : (this._buttonAssistWindow && this.buttonAssistWindowRect().y > 100) ? 0 : this.buttonAreaHeight()
Changing it into:
var wy = (Utils.RPGMAKER_NAME == "MV") ? this._helpWindow.height : (this._buttonAssistWindow && this.buttonAssistWindowRect().y > 100) ? 0 : this.buttonAreaHeight() + this.helpAreaHeight()
Okay, I have this one fixed in a slightly more elegant way.
As it turns out, the check I was using to see if the help window was on the top or bottom of the screen was checking if the Y value of the help window was > 50, which it turns out, with the button frame from VS turned on, is actually at 52, which caused the result item and recipe list window to draw expecting the help window was at the bottom of the screen.
The update is live now, feel free to download it, if you like. I appreciate your input and patience on this, I am one guy, after all, and the giant scope of this plugin, combined with testing it for several unique use cases makes squashing all of the bugs a little difficult.