I have paks 128, 64, 64.japan, 96.comic, Hajo, & HD, but I am not sure which one is best to play, are any of the ones I have best to play, or is the best one to play one that I don't have.
You should play with all eventually. But paks 64 and 128 are probably the best to start with to understand the game
Ok, but which pakset have autobahns/motorways, and elevated highways, or do I have to get addons for autobahns/motorways, and elevated highways? (I am mostly focused on Simutrans's Road Tools, Map Editing Tools, Special Construction Tools, and Elevation Tools.)
I don't know situation in pak64 but pak128 has elevated roads - but it is needed to download nightly (http://nightly.simutrans-germany.com/) set.
pak96.comic have an autobahn and elevated autobahn, and the map editing tool is easy to access. But there's no airplanes on it.