Dealership should be able to look both of those up, the door one might be discontinued, if so, hit up the parting out section here in the classifieds. Metal clip one will def. still be available.
The caps are harder to find. I ordered some recently and the brown were out of stock. Part number is 90950-01800, check the color you are ordering on whatever website.
Plug, hole (for front door trim board) 90950-01800XX
»the XX stands for the trim color. "B0" is dark grey.
I'll leave it up to the crowd to fill out the suffix list.
The clip is either
90183-05103 (nut), or
90179-06127 (listed as "bracket for front lisence plate mounting", but it's in the dash)
I can't tell which, but neither is very expensive and both are used on the dash. FWIW, this is a common Toyota part and you can find loads of them in a yard in any Toyota dash. I pick up handsful of them, and misc. screws, everytime I wander through a yard. They ususally don't bother to charge for them.