First, that is horrible. Sorry about that.. nothing worse than someone destroying a person's sense of space and security.
Well. You have a couple options. Do you have renters insurance? Homeowners? If so, they may pay for you to have the locks professionally redone at a dealer. Because the incident occurred at home, in your garage, the theft and the results of the theft can be covered by both car or homeowners. I am LESS sure about renters... and obviously, it depends on specific language in your homeowners.
I figure, since it is a 90', you probably do not have comp car insurance (makes sense) and only liability. Liability won't cover this... but if you have ANY form of home/renters, I suggest you call your agent and inquire.
Second. You COULD throw an engine kill switch on there, so even if they got in, they couldn't start it.. but that is not my personal opinion the way to go.
In this case, you are going about it the right way. You need to have it re-keyed.
My guess: Local teens.. punks that saw low hanging fruit. Had my very nice Mtn. bike rim stolen... and then, suddenly saw a very similar tire sitting in the garage next door.
If you DO grab all new locks/ignition set off a junker; make sure to grab the VIN from the truck it came from so the dealer can cut you keys. They usually require you to prove ownership via a title. A junk yard is required to have the title to take possesion, or get it... salvage. I have sold a few of my cars to yards and always signed my title to them.
If that isn't possible... Toyota "hides" the special key code on the truck. I had a 90' runner made in Canada, sold in Canada that someone brought to the US. I needed a new key made and Canada Toyota didn't keep records as long as US Toyota did, so they told me about the spot on the Truck where the unique KEY code is.
That CODE, when punched into ANY official Toyota key maker and ANY DEALER in the world... will tell the machine exactly how to cut the key. You do not NEED to prove ownership to do it this method. All they do is walk to the machine, type in the code and the cutter goes to work... the key worked perfectly.
On my 1990 4runner, the key code was stamped on the front passenger door key cylinder.

Or a part connected to it.. I forget exactly, been a few years. Easy to get to.
Test on yours. Pull the door panel off your truck's front passenger door and pop the door lock cylinder off... it will be easily readable. Stamped code, 5 or 6 digits long. (Don't quote me on exact length, again, been a few years).
I have a sneaking suspicion that models print them in the same spot.. it would be prohibitively expensive to do EACH vehicle differently. Instead, I bet they pick a spot for each model and model year and set up a machine to give each car a code as it goes through production.
I could be wrong.. but I am willing to be your 1990 4runner, and one at a junk yard will have the code stamped in the same spot.
If that is the case, you can go to a pick and pull junk yard and pop the ignition and door lock cylinders and then take that code to the dealer and have them cut you keys to it.
This method would take a bit more time, but would probably be the cheaper route...l..