Provided the breakout cables and RG6 cables used BNC connectors between them, this would clearly have the higher capacity. However, if the VGA cable at 40' was "good enough", the additional capacity of the RG6 might not make any difference. Someone who knows more than me will have to provide that info.
I have 2 runs of about 45 ft of Extron "mini hi-rez" which has five internal high bandwidth conductors. This allows me to run RGBHV off one and component plus S-video off the other. I ran the cable on the recommendation of Definitive Audio in Seattle; they did the terminations which are a proprietary BNC connector supplied by Extron, since it requires special tools. Extron also makes BNC to RGB cinvertors, and BNC to S-video convertors. This permits you to run less cable with more options.
40' is by no means a long run. Any good quality coax cable will be fine. There are also plenty of VGA Cables out there that have the same quality Coax as you would find in a seperate RGBHV bundle as well. Call any of the PRO av dealers in your area. a 50' VGA or RGBHV 5 wire lists for about 100$
If you want to go really crazy, got for an RG6 equivalent. THe extron version lists for 330$ but there are also plenty of other types out there. But the smaller cable should be fine.
www.pccables.com has guarantee not to ghost even at 50 feet. However, it's only triple (RGB) coax and not 5 coax like other high quality cables. Of course H and V does not need as much shielding IMHO. You can always get a VGA booster to make sure you don't lose any signal strength. Try not to be near any flourescent light fixture or electrical lines. If you do have to cross some try to do it at 90 degree angle. Wrapping your cables with aluminum heating/cooling tape will also shield out interfernce (or a metal conduit). It's best to run your current cables through a 2-3" flexible conduit to allow future cabling pulls in case the technology changes.
Flexible is available in larger sizes at commercial electrical supply stores and goes by the generic name of " smurf tubing". It's blue in color and comes by the foot on large spools. A common brand is Carlon, but I looked all over the Seattle area, and the largest diameter I could find was 2". I did a major AV wiring project in my own house, and used a lot of both rigid and flexible conduit where I could for future proofing. The best way , if you can , is to run the empty conduit along side of the cable runs so you can fill it as you need, and size it for the largest conductor you think you may need- DVI at present, because of the plug sizes. It is easier to pull wire through rigid grey PVC conduit, but a real pain to put that in unless it is new construction.
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