The Nishiki Prestige is a fine bike. You are starting with a good base.
+1 to the comments about checking the frame. The string test is a good first action.
By starting with a raw frame, you have chosen a relatively expensive path, but as you are already reckoning, it gives you virtually unlimited choices on your complements, and the finished product will truly be your own creation. Good luck with your build, and in finding the best components at the very best prices.
Don't discount new parts either - Wider Nitto Noodle bars and Tektro or new Diacompe brakes with Koolstop pads may be good choices for you.
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