So i bought the best house in Skyrim, Riften, i'm joking, i have no idea if it's the best, but i want to know, all the stuff that i take like the soul gems in the the enchanting room, will they respawn? because i think they are cool looking decoration, yet i'm running a bit short on soul gems... so do they?

In your house they do not.

And an additional point, if you add new ones later to replace any you took, it is nigh impossible to put them in the position the originals were in.

The 'drop them on the floor, then go back in and place it ' trick seems to help that problem. If I use that method, it normally works 3/4 of the time. Sometimes I have to change its spot a couple times before it decides to stay, especially if its in an open container like a basket or one of those troughs on the floor.

Im eagerly awaiting the decoration mod like they had in oblivion...you were able to lock items in place after you placed them as well so even if you ran into them they would be glued in place. Once that mod comes to skyrim I will be spending countless hours decorating my homes lol

One issue that does happen is the game resets the "Clutter" after a period of time. You can see this if you knock a food item or plate on the floor. After a period of time, it will be back where it was. What happens is, the clutter being put back can knock off other things that you put on the shelf or table.

I don't know happens if you just remove the clutter, say putting it in a container. That might reduce the game's tendency to move things around in your house.

What about the plants in the garden? I'm tempted to harvest them for alchemy, but they do look nice

All movable things in your house will respawn if you are away from that cell for more than the respawn time.
It seems to be at least one month.

I have gotten fresh ingredients from houses I just never go into except to collect them once a month.
The Archmages quarters is really good for this.