Hi, can anyone advise on which books have upgrades possible for speeder bikes (not podracers)?

I've seen the EOTE Core book, Fly Casual and Special Modifications. Anywhere else?

Also, how have people handled mounting weapons to speeder bikes? I've ruled any Ranged (Heavy) personal weapon can be mounted for 1HP, but this will make the bike extremely illegal for civilians, equivalent to mounting a machine gun to a motorcycle.

One final question, how much Encumbrance does a speeder bike take aboard a freighter?

Some are in Jewell of Yavin adventure as well.

yes, JoY has mods from 0 to 1 HP specific for vehicles of Silhouette 2 or less. Basically better guns, strain threshold and speed. For the Cloud Cars, you could strip armor for more speed to, so I imagine that you or your GM might allow that.