Thanks Henrik,
I was concerned that stopping the timer and restarting it would throw off the measurement, as I am sure it would. I tried it with just clearing the timer registers and tested it, and all seems good. Just checking for a timer overflow which if occurred will exit the capture routine.

Code:
  TMR1H=0      'Clear 8-bit register                              
  TMR1L=0      'Clear 8-bit register
  T1CON.0=1    'starts timer  
  overflow=0   'Clear overflow bit
  capture=0    'Clear Timer
Trash:
  If Capture = 0 then
     if overflow=1 then 
       rpm=0
       T1Con.0=0  
       return
       endif    
    Goto Trash          
  endif
  TMR1H=0      'Clear 8-bit register                              
  TMR1L=0      'Clear 8-bit register
  Capture=0    'waste first capture
  Overflow=0   'Clear overflow bit     
CaptureLoop:
  If Capture = 0 then
     if overflow=1 then 
       rpm=0
       T1Con.0=0  
       return  
       endif  
    Goto CaptureLoop
  endif
T1Con.0=0  
period.LowByte=CCPR1L
period.HighByte=CCPR1H
  TMR1H = 0
  TMR1L = 0
  Capture = 0
  Overflow = 0