Cylinders misfiring

My 98 Tacoma V6 4X4 recently started running rough. It started with just a slight misfire. Yesterday, it was driving fine for about 5 minutes then became very rough. The check engine light came on so I had it diagnosed. Cylinders 1 and 2 misfiring along with a random cylinder misfire. Timing belt (chain) was replaced a few years ago so I don’t think thats the problem. Any ideas??

Well, the first thing to worry about is the simplest - have a look at the ignition system components - plugs & wires at minimum.

I forgot to mention that it will run fine when I start it for about 3 minutes. Then the roughness begins

I would start by making sure it’s up to date with all the maintenance specified in the owners manual.
Then I would suspect ignition parts not changed on a scheduled basis, like the plug wires, coil(s) and ignition module.
Next I would do a compression test and check out the EGR system.