Here are the production numbers for each year, model, and color from the "CVO Numbers" thread in General Discussion. The per-market breakdowns are also in the thread, but back a few pages. I posted them nearly a year ago. I've even included the numbers for the VRSCX and the Destroyer, which aren't technically CVOs.
CVO PRODUCTION NUMBERS
1999 FXR2
Arresting Red 625
Stone Cold Blue 276
1999 FXR3
Two-Tone Candy Emerald Green w/Flames 621
Two-Tone Bright/Dark Candy Blue w/Flames 300
2000 FXR4
Screaming Yellow Pearl/Eclipse Graphics 664
Candy Tangerine/Eclipse Graphics 316
2000 FLTRSEI
Vivid Black/VR Racing Orange/Arctic White 793
Three-Tone Red 768
2001 FLTRSEI2
Vivid Black/Platinum Silver/Charcoal Satin Bright 858
Sinister Blue Pearl/Diamond Ice/States Blue Pearl 849
2001 FXDWG2
Scarlet Red/Gold Flames 1,676
2002 FXDWG3
Navy Blue Pearl/Silver Metallic Flames 1,011
Vivid Black/Gold Flames 935
2002 FLHRSEI
Purple w/Flames 1,771
Candy Brandwine w/Flames 408
2003 FLHRSEI2
Centennial Gold/Vivid Black/Burgundy 3,603
2003 FXSTDSEI
Centennial Gold/Black 3,080
2004 FXSTDSE2
Candy Cobalt/Starlight Black 1,296
Yellow Pearl/Platinum Mist 1,028
2004 FLHTCSE
Candy Cobalt/Starlight Black 1,561
Orange Pearl/Jet Black 1,293
2005 VRSCSE
Electric Orange/Black 1,097
Two-Tone Light Candy Cherry/Dark Candy Cherry 790
Two-Tone Light Candy Teal/Dark Candy Teal 446
2005 FLSTFSE
Electric Cherry/Vivid Black 1,528
Platinum Mist/Charcoal Slate 1,290
Candy Cobalt/Starlight Black 858
2005 FLHTCSE2
Two-Tone Light Candy Cherry/Dark Candy Cherry 1,874
Sunrise Yellow Pearl/Stingray Silver 1,053
Two-Tone Light Candy Teal/Dark Candy Teal 693
2006 VRSCSE2
Scarlet Red/Charcoal Slate 918
Electric Orange/Black 796
Chrome Yellow Pearl/Platinum Pearl 523
2006 FLSTFSE2
Autumn Haze/Abyss Blue 1,414
Concord Purple/Canyon Copper 1,189
Nebula Yellow/Cobalt Blue. 1,029
2006 FLHTCUSE
Black Candy Crimson/Charcoal Slate 1,901
Autumn Haze/Vivid Black 1,313
Black Emerald/Majestic Green Pearl 574
2006 VRXSE
Two-Tone Inferno Orange/Black 646
2007 VRSCX
Two-Tone Mirage Orange Pearl/Brilliant Silver Pearl 1,290
2007 FXDSE
Inferno Red/Desert Black 838
Silver Rush/Midnight Black 767
Twilight Blue/Ice Blue Pearl 645
2007 FXSTSSE
Canyon Copper/Candy Red 1,027
Abyss Blue/Blue Pearl 991
Amarillo Gold/Candy Tangerine 540
2007 FLHRSE3
Black Ice/Pewter Leaf 1,357
Razor Red/Burnt Gold Leaf 1,115
Candy Cobalt/Pale Gold Leaf 855
2007 FLHTCUSE2
Black Ice/Electric Orange 1,930
Light Candy Cherry/Black Ice 1,453
Lightning Blue Pearl/Midnight Pearl 744
2008 FXDSE2
Scarlet Red Pearl/Dark Crimson 721
Candy Cobalt/Midnight Blue 609
Crystal Copper/Black Onyx (Anniv) 961
2008 FXSTSSE2
Black Diamond/Smoked Candy Flames 871
Inferno Orange/Fireburst Flames 716
Crystal Copper/Black Onyx (Anniv) 921
2008 FLHRSE4
Black Diamond/Silver Dust w/Ghost Flames 1,072
Twilight Blue/Candy Cobalt w/Ghost Flames 620
Crystal Copper/Black Onyx (Anniv) 1,535
2008 FLHTCUSE3
White Frost/Silver Mist 1,211
Canyon Copper/Stardust Silver 1,335
Crystal Copper/Black Onyx (Anniv) 1,731
2009 FXDFSE
Black Diamond/Fire Quartz 965
Denim Granite/Electric Blue Fade 512
Sunrise Yellow Pearl/Platinum Quartz 342
Electric Orange/Slate Black 179
2009 FXSTSSE3
Black Diamond/Emerald Ice Flames 995
Candy Cobalt/Blue Steel Flames 762
Sunrise Yellow Pearl/Volcanic Fury Flames 410
2009 FLTRSE3
Electric Orange/Vivid Black 1,605
Stardust Silver/Titanium Dust 1,386
Yellow Pearl/Charcoal Slate 517
2009 FLHTCUSE4
Ruby Red/Typhoon Maroon 1,155
Stardust Silver/Twilight Blue 1,105
Autumn Haze/High Octane Orange 622
2010 FXDFSE2
Cryptic Black/Hellfire Flames 242
Satin Pewter Denim/Sandstone Grind 116
Opal Blue/Hellfire Flames 57
2010 FLSTSE
Inferno Orange/Vivid Black 829
Crimson Red Sunglo/Autumn Haze 589
Abyss Blue/Sapphire 503
2010 FLHXSE
Spiced Rum/Gold Leaf 1,652
Candy Concord/Pale Gold Leaf 1,038
Tequila Sunrise/Pale Gold Leaf 744
2010 FLHTCUSE5
Burnt Amber/Hot Citrus 794
Scarlet Red Pearl/Dark Slate 747
Riptide Blue/Titanium Dust 569
2010.5 FLHTCUSE5
Crimson Mist Black/Dark Slate 992
2011 FLSTSE2
Maple Metallic/Roman Gold 718
Scarlet Red Pearl/Dark Slate Pearl 596
Midnight Sky/Candy Cobalt 578
2011 FLHXSE2
Black Diamond/Crimson 1,386
Black Diamond/Inferno Orange 987
Kryptonite/Black Diamond 874
Autumn Haze/Antique Gunstock 482
2011 FLTRUSE
Rio Red/Black Ember 1,338
Charcoal Slate/Black Twilight 1,213
Frosted Ivory/Vintage Gold 346
2011 FLHTCUSE6
Black Ember/Rio Red 1,481
2011.5 FLHTCUSE6
Twilight Blue/Candy Cobalt 932
2012 FLSTSE3 SOFTAIL CONVERTIBLE
Crimson Red Sunglo w/Scarlet Crystal Graphics 651
Satin Pewter w/Catacomb Graphics 538
Abyss Blue w/Catacomb Graphics 438
2012 FLHXSE3 STREET GLIDE
Dark Slate/Black Diamond w/Phantom Flames Graphics 1,753
Hot Citrus/Antique Gunstock w/Phantom Flame Graphics 1,373
Ruby Red/Typhoon Maroon w/Phantom Flames Graphics 1,043
2012 FLTRXSE ROAD GLIDE CUSTOM
White Gold Pearl/Starfire Black w/Real Smoke Graphics 1,238
Maple Metallic/Vivid Black w/Real Smoke Graphics 799
Candy Cobalt/Twilight Blue w/Real Smoke Graphics 602
2012 FLHTCUSE7 ELECTRA GLIDE ULTRA
Electric Orange/Black Diamond w/Big City Lights Graphics 1,493
Wicked Sapphire/Stardust Silver w/Big City Lights Graphics 1,193
Crystal Citron/Diamond Dust w/Big City Lights Graphics 663