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The dry transfers can go on at any point in the process. A clear coat once they're applied will help protect them. The decals will want at the very least a semi-gloss (satin) surface to adhere properly. I'd apply the semi-gloss (or gloss), apply the decals and dry transfers, then overspray with the semi-gloss, matte, or whatever finish you want. If it's a passenger car or locomotive, I'd opt for the semi-gloss or gloss, as those tended to be kept in good repair. The freight stuff would likely be much more of a matte finish.