Ooops. Sorry the spec is 0.005 and 0.011 (+/- 0.001)for the intakes and exhausts, respectively. Sorry, had a brain fade for a second.
Do you have a service manual or equivalent? This is a key item in performing any manitenance or repair for these bikes. I highly recommend any service manual (Clymer, Haynes, etc). The official Honda service manual can be ordered from here:
www.helminc.com
The answer to your last question is neither.
First, let me clarify since I made a mistake earlier. Your right intake clearance being 0.004" is not out of spec. You are however on the line. Since the spec allows for +/- 0.001". If everything fails normally (huh?

), those clearances will decrease with wear. This will require the need for a thinner shim to open the clearance back up.
The formula:
A=Measured gap
B=Specification
C=Old shim
D=New shim
(A - B) + C = D
Clear as mud?