i am new to the Boxster but an old 993 guy. Bought a 2000 986 Boxster and perused the forum here without any real definitive results on best clear side marker lights to buy and how to change out front and rear yellow lights. I understand the front headlights maybe need to be entirely replaced to accomplish because they are one piece? What about rears?

Any help and advise on best best way and product to purchase much appreciated!

Welcome to the Boxster world! I too am an old 993 guy but even older 986 guy and now enjoy them both lol!
I changed the front lights on my 2000 986 to the bi-xenon or lightronics years ago due to bad discolouration of the standard lenses and they only come with clear signal lights. I then needed to purchase little triangular pieces also in clear to fill a spot beside the signal light, these either have or don't have spray nozzles for the headlights. I also purchased the side marker lights in clear because of their proximity to the front lights to keep it all the same. All these pieces were bought from the local Porsche dealer. Ive chosen to leave the rear lights as they are but I think they are an easy swap if you choose to do so.

Amaon head light replacement set

Amaon head light replacement set

I would imagine that LED exist but when I did mine 8 or 9 years ago my only choice was OE non LED.

Yes, litronics are expensive and probably not worth it if yours are not yellowed inside, mine were quite bad. Also given the market value of a Boxster these days it's a lot to spend🙁.