I got an R1 2002 shock and want to replace the standard one, but the R1 shock is 46 mm shorter its mean that the all bike will be lower with 46 mm and its not the point ,Is it anything I can do ?

 

Well lol you could...

A) get a shock that fits...

DMr Performance Suspension ? Performance Motorcycle Suspension and Chassis


Or if that's not in your budget you could...

B) google it to see if anyone's done it before...

R1 shock fitted with pics - VTR1000.ORG


'99 and '02 and two different part #'s (cross reference the part #'s on the Ronayers or Partzilla microfiche). I'll pass the ball to you from here and let you continue searching to compare shock lengths and go from there...