Well, let's see, here:
"I am guessing that I have to run seperate grounds to the various items I want to work, like tail lights and headlights, blinkers."
Yes, but you can "Daisey Chain" some of them for convenience, For instance, you can run a single ground wire (12 gauge or so) to the tail lights (including their directionals) and the center license plate/backup light. Just use a crimped-on ring-lug on one of the mounting posts for the light and run two wires to the lug - one from a good chassis ground somewhere (I used the rear frame on my CMC) and the other to the next light, then another from that light to the last across the back.
I have separate grounds to EACH headlight (I'm also running 100 watt headlight bulbs!!), and then run a 14 gauge ground wire from each headlight to a corresponding front directional. You may also find that the parking lamps inside your headlights want a separate ground, too, depending on where they come from.
"Is this a simple ground wire to the metal subframe that is ground to the battery using ground straps?"
I'm not sure what you're asking here, but you should have a good, 12V ground cable from your battery ground to a SOLID part of the pan or frame, securely bolted on with a stainless steel, 5/16" dia. bolt. I use a 7/16" diameter piece of welding cable, but a ground cable from Autozone would probably be OK. Then you may attach other ground points to the pan/frame where-ever it's most convenient. I have two at the front (for the headlights) another at the rear (for the rear light cluster) and another up under the dash (for the dash lights/gauges).
"I am going to be mounting a 3rd brake light LED light and the strip has a ground wire attached as well as the hot. Does the ground have to go to the frame or engine or can I use the existing tail light or brake light ground?"
Yes, you should attach the LED ground to the frame, preferably NOT the engine as the engine moves while running and is just harder to attach to. For something like a third brake light, you can get some double-lead-wire from auto stores as used for trailers and such. DO NOT use speaker wire or appliance "zip-cord" as the insulation can't take the heat in the engine compartment or near the exhaust system. Teflon coated is best, but harder to find and more expensive, while better PVC coatings can take the heat. Using the double-wire stuff makes for a neater installation.
Hope this helps.......
Gordon (Dr. "Sparks")