The stock caps feature a 90-degree bend and fit a CR8E spark plug with a 10mm base and stud-type terminal. This lends to the NGK resistor covers with the model number LD(resistance)F
The 10K ohm spark plug cap would be NGK LD10FH (LD10F). <- Though these are difficult to find.
Yamaha recommends using replacement caps (PN 4BP-82370-00-00) which cross references to an NGK 8060 (LD05F) which is a 5k ohm resistance plug cap. The NGK 8060 is black in color. A red cap is also available (NGK 8231).
The dimensions and specs for the LD05F are as follows:

You can find more information on the resistor caps from NGK:
http://www.ngksparkplugs.com/docs/Resistor_Covers.pdf
The OE Yamaha part number for the plug caps is 4BP-82370-00-00. They list for $29.33 each.
You can purchase the NGK 8060 and 8231 at several online stores for $3.50 each.