The velodyne PCAP is a stream file. It's like a video stream with a counter. You need to know or figure out where the camera is at every given moment. The Trajectory gives you that information before you process and SLAM figures it out with the raw data.
Add a GPS/IMU to obtain a trajectory, then align the counter to the GPS time and use software other than LASTools to create a point cloud. Not sure if there are any open source solutions available. (I process in this manner with a velodyne HD32e with software from LiDARUSA. They put together the program to align and process the PCAPs.)
Or use a SLAM algorithm (check out OpenSLAM.org) which uses something like a 4d photogrammetry solution to piece it all together. LASTools will not provide these results.
Once you have your cloud, LASTools comes into play to translate, manipulate, classify, resize and otherwise. See the LASTools documentation for the various functions.