First, buy this book...
https://www.themotorbookstore.com/porsche-986-boxster-boxster-s-service-manual.html
Then:
1) if you have 100k on the motor there is a reasonable chance the IMS was done. At that mileage I might consider just doing the Pelican kit and call it a day. Many opinions and several options. Do the tensioners as well.
2) if you are throwing smoke, do the AOS first. Haven’t done it, but it seems the pinch clamp is a Biotch to get to... other than that, not so bad. Use a Porsche unit, not aftermarket.
3) struts are most likely shot, might be worth a Porsche specialist to take a look see at the front and rear and get a good take on the suspension components if you don’t know what to look for and replace as necessary. Struts, probably springs and mounts is where I would start.
4) refresh your trans oil with the Porsche Unicorn Blood (not on your list but worth doing)
5) when and if you need to take a look at your window regulators/micro switches remember you have side airbags...
6) if I needed to do a top, I would probably look for an 03/4 glass rear window full setup off of a donor car, I think there are some minor mods that need to be done for install, but then you get the headliner and all the goods. Or, source a hardtop, they are usually around 1k give or take. Actually reskinning one without experience looks daunting, but doable. I did several targa tops a long time ago, those could be a pain. Not sure if I would tackle the top on the Boxster...
Have fun. Sometimes with projects the $$$ spent makes absolutely NO sense, but at the end of the journey you have something you built, and that can be value enough.