Need some help

[redwing24]

I been working on a 2000 IS, been sitting several years.  Pulled carbs, cleaned jets and installed new float valves after first try. Put carbs back on wi4h air box. Using aux gas tank.  Started her up today and she ran with no gas leakage.  But she seems to be skipping.  When i pull the plug wires to 3 and 5 i get no change in engine running, when i remove plug wire from others engine changes.  Check plugs and they are working and new, checked and i have spark on both, but it doesn't seem to be as strong as others.  Thought it might be coil but they  come off of different ones. 

Any suggestions where to try next?

[98valk]

test plug wires for correct resistance. all have a resistor in the plug caps. they do go bad, although rare. can be changed out. check all plug/wire connectors for corrosion.
make sure none of the plugs have corroded threads in the well.
this is a wasted spark ignition system, meaning some plugs will have a slightly weaker looking spark than others.

[Bigwolf]

  When i pull the plug wires to 3 and 5 i get no change in engine running, when i remove plug wire from others engine changes. 

That sounds kinda strange!  When you pull plug wire off number 3, both cyl 3 and cyl 4 would cease to function.  Likewise, when you pull number 5, both 5 and 6 would cease to function.  I believe you are trying to describe it as running on more than just 2 cyls but what you are saying would make it seem that it is just 2 cyls running.

I would suggest following what CA suggested and you might also want to check the fuel bowls on carbs 3, 4, 5, and 6 just to be sure they are filling correctly.  Since you just had the carbs off and seem to be having a problem with 4 cyls even though they do have some spark, I would suspect the fuel system first.  I am assuming that you did a good job of prebalancing the carbs while on the bench.  However, a good carb balance on the running engine is best.

Bigwolf

[Red Diamond]

Pull the carbs again, install new high and low speed jets (stock), take care of all vacuum leaks, sync the carbs after reinstall, you're good to go. You may think you did a good job cleaning the jets, but after setting up for a long time they need to be replaced. That is what causes the mentioned cylinders to misfire. You can order new jets from Jets R Us, I think it's Jetsrus.com

[Hook#3287]

The first and only time I cleaned my jets, I didn't and had to pull the carbs again to replace them.

Some have stated they've had good luck cleaning jets, but I just as soon replace with new, than do the carbs pulling thing twice.