Hard top fitament...Will a 1999 hardtop
 

fit a 2003s?

To my knowledge all of the 986 (97-04) style hardtops fit... do not think the top is any different for an S unlike the convertible one which had a liner included.

It will fit just fine.

The fit will be fine although you might need to make some adjustments to account for differences between your car and the donor car.

If I recall correctly, there is some titanium-colored trim on a Boxster S that is not present on a standard Boxster. I believe a hardtop that came originally with a Boxster S has titanium trim around the rear window. This is not present on a non-S hardtop.

Most people won't notice.

There were 2 versions of the hardtop
 

different because the early one had little flaps just back of the side window made IIRC for the mounting of a top carrier that Porsche sold but few used. The later version of the hardtop has a smooth one piece look just back of the side window.

Both versions mount the same and either will fit all years of the 986.

You will need what are called spinlocks to mount the top. See if the seller will give you those in the deal.

Cost to paint to match body? - Or do some just mix and match?
 

I guess a black top could be used on several body colors - but if silver or white I assume it would need to be painted.