For acceleration/deceleration settings see:
Make sure the machine is mechanically sound. Per the machine operating checklist: Machine operating checklist , the basic points of adjustment for a machine are:
Pulley set screws — verify that these are in-place and secure — for further details on checking them on a Shapeoko 3 see: http://docs.carbide3d.com/shapeoko-faq/shapeoko-3-how-to-check-the-pulley-set-screws/ — be sure to check all axes/pulleys (including Z on machines w/ belt-drive Z-axis, for an HDZ, check both coupler screws).
(for the SO3/4, X- and Y-axes) V wheels / eccentric nuts: Tightening Eccentric Nuts - Carbide 3D
(for the Pro, and SO4 Z-axis) Lubrication of the linear rails: Getting Started with Carbide Machines
Belt tension (see the relevant step in your instruction manual, e.g., Getting Started with Carbide Machines) Note that the X-axis motor is held in place on standoffs and if those bolts are loose this can cause belt tension issues. Also, belt tension for the Y-axis stepper motors needs to be even/equivalent on each side — a significant difference can cause skipping on one side eventually resulting in lost steps on both. Measuring belt tension, squaring and calibration
Ensure that all screws are in place and secure, esp. on the linear rails on a Pro.