Holy smokes... so I found my Santa Fe engine that I had stored in a box but I'm missing a few pieces: 2 light grey bars, 1 3x3 light grey round corner, and 1 9v light grey decorative side. The one hole in the red base plate cracked as I had the 9v motor attached to it and was on its side the whole time and two of the grey 2x3 curve tops are scratched. So I want to replace those 3 pieces. Anyway, bricklinking them is gonna cost me 40 dollars! Should I even bother getting these pieces or should i just sell it as is on ebay?

That's awesome that you found that set! That is one of the most sought after Lego train engines out there. If it were me I would spend the $40, replace the parts and keep it, but if you're just going to sell it then it may not be worth spending the $40. You will still be able to get a lot of money for it, even with the missing pieces.

Holy smokes... so I found my Santa Fe engine that I had stored in a box but I'm missing a few pieces: 2 light grey bars, 1 3x3 light grey round corner, and 1 9v light grey decorative side. The one hole in the red base plate cracked as I had the 9v motor attached to it and was on its side the whole time and two of the grey 2x3 curve tops are scratched. So I want to replace those 3 pieces. Anyway, bricklinking them is gonna cost me 40 dollars! Should I even bother getting these pieces or should i just sell it as is on ebay?

Great little set. Keep it.