Keep looking for vac leaks.
Big ones: In/Ex manifold, where insulator/heat shield meet intake manifold, where insulator/heat shield meet base of carb, insulator on carb that goes between the bottom and middle plate, any connection that goes into the intake manifold.
You said you have now replaced all the vac lines for the emissions, right?
Double check that they are all routed correctly. No open or broken lines. Double check the BVSV mod.
Do the Emissions Manual check for each emission component (don't need to do the Air Injection or any system that doesn't affect ignition or fuel- on BVSVs, just check the routing or bypass them, don't pull them off to check them). It looks overwhelming, but it really doesn't take that long, once you become familiarized with each system.
Also, in the throats of each barrel in the carb there are small holes in the walls. When you did the carb rebuild, you should have been able to spray carb cleaner through those and the slow jets. Try spraying those good with carb cleaner using the plastic hose on the can of carb cleaner inserted inside the hole (with the engine off). They might be clogged and that is why your idle mixture screw is not responding. Don't drop the plastic hose down into the manifold. If you have ever bought Seafoam, it comes with a curved red plastic hose. That might work better than a straight one, because the opening to those holes in the barrel walls might be pointing down.
Once you are convinced lines are routed correctly and the emissions components are working properly and to the best of your ability there are no vac leaks, reset timing as close to 7* BTDC and get the best idle you can get on the carb.
Then I would do a valve adjustment. When was the last time the valves were adjusted?
If you have never done one, double team with your buddy who help you do the other stuff or with someone else who's done it before. Don't overtighten the exhaust valves, they are going to get tighter with time.
see links for full procedure on setting the valves:
https://forum.ih8mud.com/60-series-wagons/489587-fj60-valve-adjustment.html
https://forum.ih8mud.com/showpost.php?p=4300965&postcount=7
When you are ready to adjust the valves, take off the flywheel housing cover underneath your rig and move the flywheel until you can see the line and the bb, then paint them both white with white fingernail polish or chalk. It will make it easier to see them in the viewing window.
Use the line, not the bb, on the flywheel when adjusting the valves; when the line on the flywheel aligns with the pointer on the viewing window, the 1st cylinder is AT TDC, and when the bb on the flywheel aligns with the pointer on the viewing window, the 1st cylinder is 7* BEFORE TDC. To get the line on the flywheel to align with pointer on the viewing window, make sure the rig is parked on a flat surface. With the engine OFF, put the transmission in 4th gear and release the handbrake. Now you can push or pull the front of the truck and the wheels will rotate the crankshaft which will rotate the flywheel until you see the line mark on the flywheel align with the pointer in the window.
Remove your distributor cap (you can leave all the ignition wires attached).
Check whether the rotor on your distributor is pointing the ignition wire on the distributor cap that leads to the 1st or 6th cylinder; if it is pointing to 1, then the 1 piston is in compression stroke and 6 in exhaust and vice versa. See the chart on page two of the link above.
