well im rebuilding my 22re and i was taking the pistons out today and there was a bad scratch on the crank and the connecting rod where the bearings were gone on my #3 piston, any ideas on what to do or should i not even worry about it

 

You can have a machine shop weld onto the journal & regrind it to original specs. You might be able to have all journals reground & use oversize bearings. If the scratch is on the first or last journal, they won't weld & regrind, but you should be able to get a reground crank. I got a reground crank when I rebuilt my 3vz-e (spun a rod bearing on journal #1). Worked great, and a lot cheaper! Let us know what you end up doing. Either way, if you reuse it as is, you'll probably end up having the same problem. Not sure about the connecting rod, you might have to get a new or used one from a scrap yard.

 

You can get a "new" (reman) crank for around $200.
Pull it out, have it checked for spec, regrind as necessary.
You should worry about it, unless you consider bearings to be servicable parts.

 

well the crank isn't so bad just light but noticeable scratches its the connecting rod thats bad but do u think it wouldn't matter since the bearings set in there

 

Can you feel the scratches?
I'd have a machinist look at it.
I won't matter until the bearings get worn. If the surfaces are scratched, they'll wear much quicker than they would otherwise.

Not turning/polishing the crank is probably the #1 problem I see with "rebuilt" motors.. These motors don't last very long, some less than 10k miles.
Connecting rods for the 22r /22re are cheap - just post a WTB.
Completely reconditioned, around $150 for all 4.
Used, maybe $10-$20 each.