Hey Mike, One thing to take a look at. Fuse #4 in the dash fuse box is called a starter signal fuse. I'm not 100% sure on Toyotas but on some other brands, notably Nissan, this circuit tells the ECU to provide extra enrichment and timing advance during cranking to help with startup. I've found the fuse missing and/or blown on numerous Nissan vehicles when I worked at the Nissan dealer. Also, there can be a fault in the ignition switch that prevents current from flowing to this circuit. To test this properly; find the #4 fuse. Using a test light, check for power on both sides of the fuse while cranking the engine. It should only have power when the key is in the start position. If both sides have power, this isn't your problem. If only one side has power, the fuse is blown. If neither side has power while cranking, you've likely got a bad ignition switch or a fault in the circuit. Hope this helps.
This youtube video can show you where fuse #4 is located. Fuse box location and diagrams: Toyota 4Runner (2003-2009) - YouTube