I would like to use the battery for the winch and also as a back up to the starter battery. I am looking at this set up the same way you would look at any dual battery set up. Only difference is that the second battery is in the nose cone of the trailer vs the engine bay.
I think you're over-complicating things.
Do you really need to combine the batteries for winching? Tons of people winch off just the single battery, with no problems. What you're suggesting is just... Rube Goldberg-ish.
What size fuse should I use?
500 Amps, for a winch and starting. At that amperage, it's entirely possible to start a fire without blowing the fuse.
The thought was to run the winch off both the main battery in the engine bay as well as the auxillary battery from the trailer.
For that, you're going to need to run something massive like 0 gauge or better, for both the power and ground, and an Anderson Connector at the back of the truck.
I had planned to run 4 awg to the trailer battery. How to I make the jump from the the back of the vehicle to the trailer? I guess I need a plug right. I can't step down to the 7 pin trailer plug can I ?
4 won't be nearly big enough to run a winch. Especially not over the 20 foot distance you need. And doing it over a 7 pin plug will melt.
Why not just do the simple solution? Do a standard 10ga/7 pin trailer setup. Install a big Group 31 battery in your truck. Carry jumper cables. A good primary battery is plenty good enough to run a winch. In the extremely rare case you need a jump start, remove the trailer battery, bring it up to the front of the truck, and use the jumper cables. This is the slightly slower, but WAY more reasonable approach to this problem.