I was where you are about a year ago. I didn't replace the window as I had a feeling it would look bad, so I replaced the whole top. Got a real nice one out of England for $500 shipped. I didn't get the glass window because a) the orange defroster lines look like crap, and b) it seriously restricts access to the engine compartment on a '99.
Next I replaced the standard seats with a pair of sport seats that I found. They cost me $1600 for the pair (shipped) but they look like brand new and I really like them. Staying with the interior, I also replaced the ugly four spoke steering wheel with a three spoke from an '03. Also got the shifter from an '03 to complete the look.
I also have some stone chips, but I got the paint buffed out for $100 to make it all shiny again, and then used color-coded wax to hide most of the chips. Looks great. My headlights were scratched and hazy, so I had those polished as well.
Mark
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'99 black 986
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