I have a 2002 4x4 ford escape v6 that is misfiring in cylinders 1,3,5. just bought it yesterday, did not give any trouble on test drive. Tank was near empty when purchased. Added fuel additive and it stopped shuddering for a good 10 minutes. Installed new air filter just in case.

SOURCE: locate cylinder number 1 on a 2002 Ford Escape

If it is a 3.0L it is the rear bank, the one closest to the pass side

if it is a 2.3L it is the one all the way to the left

SOURCE: 1991 Isuzu 4X4 Pickup 3.1 V6 won't warm start plus shudder in low

Your flywheel sound like it has hot spots on it, making the clutch chatter. You might need to pull the flywheel off and get it re-surface. This is like turning your rotor, or brake drum. If you pull the flywheel, you will see discolor spots on your flywheel. This is called hot spots, and will make the clutch slip.

On the other problem, have you changed to fuel filter and fuel pump. It almost sound like your running out of fuel????

SOURCE: 2002 ford escape v6 misfire after washing engine

coil packs got wet take wires off and put dialectic grease in the boot ends

SOURCE: 2006 RAV4 V6 multiple cylinder misfire, VSC, check engine and sli

You need a scanner to pull out the engine light codes.
Use a shopu manual to aid you with the diagnosis and repair.
The slip indicator and vsc light being on means these systems are not working. Once you pull the codes and do the repair and erase the codes the lights will go off.
There will be a code in there for the misfiring.
Good luck and keep me posted.

SOURCE: Check Engine Light on Yr2001 Ford Escape V-6 2wd.

If the engine has a P0305 DTC (Data Trouble Code) for a "cylinder 5 mis-fire detected", then the first thing to do is to do a compression test to determine if the mis-fire is actually being caused by a mechanical problem, or an electronic problem.

If the engine really does have low compression on the #5 cylinder then that is caused by a mechanical mis-fire and nothing electronic will repair it, and the most common causes for a mechanical mis-fire would be a burnt or bent intake or exhaust valve, a warped cylinder head or damaged head gasket, or a damaged piston. You can call around and find a repair shop that will do a "compression leak down test" if you want to know exactly what is causing the compression leak without any dis-assembly to the engine.