My '96 lincoln mark viii runs rough and i put a obd II reader on it and it said "cylinder 5 misfire" and i have changed the spark plugs and wires. Now i am not sure what to do. Also there is a knocking sound comming from the front driverside wheel when i am driving.

The knocking can be from #5 cylinder which should be the front cylinder on the drivers side.
You should disconnect the negative battery cable for 10 minutes and see if the reader says the same thing after you restart the car.

If it does not cure the problem, it could be the coil pak for #5. The last thing would be a dirty or bad injector for #5. Hopefully the reader will show you fixed it.

The knock you refer to can easily be a balljoint or tierod end. If you are due for a frontend alignment those are parts which will be checked before an alignment can be done.

Good answer above. Be sure to check all your vacuum lines again too.

The knocking under hood sound could be the stabilizer bar bushings wearing out. Some owners replace just the bushings Easy job. I went with Moog grease-able stabilizer bars for about $33. I had a shop do it, was about $80 bucks labor.. Mine were original 1994. REAL worn when I bought the car. It knocked very loudly and annoying over the bumps. After the fix, no more noise.