However, I did upgrade to the AE version, and, ever since, I've been having issues.
When you say AE version, do you mean SE? Or is this Anniversary Edition or something? All your mods, SkyUI and SKSE have to be for the edition you are running.
My most recent issue is that the mouse buttons does almost nothing in the menus, and if I get a dialog box in them, like the box in the character creation screen that asks if you want to save and name or continue creation, I am unable to select either option. The cursor moves and highlights the appropriate option, but will not allow me to click and select.
I have had issues with character creation, where the mouse cursor does not actually hover over the selection and I have to click under it and to the right. The most irritating thing is when selecting race, I click OK or whatever it is and it jumps up to the race above. EG, when choosing Orc I have to pick Wood Elf, and it then jumps up when showing the character to show an Orc.
So how do I play a Wood Elf? I think I disabled all the mods and set Controls to Vanilla, went on the cart to Helgen and manually saved with a console command "Save Vanilla_Start"
But when using this Vanilla_Start save with my customised controls, same problem. So I have to load an old save and reset all the controls to default when starting a new game with a different race.
But I never have a problem in the actual game with highlighting a dialogue option and selecting with a left mouse click. Well, sometimes, it selects an option higher up in the list when talking multiple times to the same Follower, so I have to be careful that it is actually highlighting the option I want, or I exit the menu and start again, EG when training, trading items, getting my gold back etc. The problem is that unused options are bright white and those I have selected and used already go grey, so it can be harder to see if a greyed option is actually highlighted.
Do you use SkyUI? As Skyrim for PC is a port from Console, I find it impossible to play without SkyUI. This makes using just keyboard and mouse much easier. But it has to be the latest version of SkyUI and SKSE for the edition of Skyrim you are using.
I'd also suggest checking your Controls settings. I set all games to run like Daggerfall, where you look is where you move, Left Mouse is Forward (I never got on with WASD), right mouse is Main Attack, Alt is Block, Mouse Left Side Button is Interact and so on.
Another thing about Skyrim (I still play SLE) is that even when using SkyUI and customising all my key binds, the game always shows the Vanilla Default option, so Interact/Steal is shown as F, even though it is actually Left Side Button (Mouse 4 or 5, depending on the mouse). In other games, my key binds override the Vanilla on-screen instructions.
IIRC, "OK" is something like Enter, so you could try using that after highlighting with the mouse if clicking with Left Mouse Button does not work. But I'd also check your key bindings in Controls settings.
Please let us know how you get on.