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Is it better to use pre-made treads or use hardwood for the treads.
Solid, factory made treads (11.5" x 1.125" x random length) are the way to go, if you can. Not always EASILY available in the more obscure exotics. But easy to get in oak (either red or white), maple, b. cherry, fir, walnut, etc. These are typically unfinished so they require finishing. If you're trying to match a prefinished floor, that can be done but it is tricky.
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Also has anyone installed base shoe in the same species as the hardwood or do you usually just install painted shoe moulding?
I've done it both ways. I prefer the look of the painted baseshoe over the look of the wood toned baseshoe but the wood tone is easier, IMO. Prepaint the baseshoe if you're going to use painted baseshoe. Then caulk and touch up paint after it's installed. BTW, you do not HAVE to spray lacquer paint again. A quality acrylic enamel can be used instead and color matched and no one would no the difference. Easier to apply and touch-up, IMO.