Today i wanted to change my leaky pinion seal and 1st,the pinion nut was hand tight.(is this normal?)
2nd, two of the five shims are damaged (see pic) can i just change the shims with new ones and put all back together?
3rd, what do i torgue the pinion nut to?

Pinion nut torque = 250-270 foot pounds.
The shims control the preload on the pinion bearings. The bearing may have been damaged when the nut backed off, allowing a no preload condition.

the bearing appears to be good, so how do i go about putting it back together? just replace the shims and tighten to torque specs? or do i need to torque using nut without the seal on?

If you are not going to change any bearings, you could replace the shims with the same size and retorque to specs. But there would be no way to accurately check bearing preload. You should be able to rotate the pinion by hand with the correct torque on the nut. If you can't, there is to much preload and you will have add to the shim thickness.

Maybe DoctorDiff will post a few suggestions.