I know you can remove the duplicates in Map Edit, but Map Edit has issues for an area as large as Texas too, it will not display all the data, nor will it save it. The duplication isn't in a single file, rather the NHD basins overlap - at least for Texas. I've got 219 basins, it would take a lot of work to figure out which basins overlapped.
As for the "dozens of clicks", I downloaded MacroExpress to help with that area. Really saves the day when working with large datasets.
So, for now, I created my separate layers in ArcMap, clipped everything down to just Texas (the NHD data also included data for Louisiana, Arkansas, Oklahoma and New Mexico, even though I specified just Texas), created a grid that covers Texas (25x35 rows) and split the coverages based on that grid.
Then I created a program in C# that would created the default .mp file and preload it with a "dummy" polygon and the default levels (Map Edit will not load an empty map). That allowed me to create all the .mp files for my tiles.
THEN I created another program that would take the "next" tile and move the SHP files over to a standard directory, that way Map Edit could always look in the same directory for it's files. This application would load up Map Edit with the current .mp file.
Then my macro would load the SHP files, specify the type, specify the layers, remove duplicates, remove the "dummy" polygon and save the .mp file. The last step would be to run the C# app I created above then start the macro over.
So, up to this point everything has pretty much been automated. Now I'm waiting for cGPSMapper to create the image files. The "automated" portion of this process has taken over 24 hours, I estimate the cGPSMapper portion to take another 48 or so hours.
I started out with 249 basins, I now have 419 tiles without duplicated data and about half the data as the basins contained since I'm only working with Texas data.. Hopefully it'll work without fits this time.
I also figured out the querystring for the NHD data and wrote ANOTHER C# app that downloaded all the data for Texas automatically. I'm a programmer by trade, so I try to find a better way to do all this repetitive stuff. If I can get the Texas data to work I'm planning on creating the data for the whole US and making it available.
IF this works I'm also planning on overlaying DEM data, but I'd also like to find reliable road, trail and rail data in SHP format. I'm trying to create a high def area and topo map for Texas that resembles the 24K topo as close as possible, the topos are a god send when hunting.