Essentially there are three, and they were all done in the early years.
1) Forward Slave Strut
2) Landing Gear Geometry
3) Stretched Fuselage
Forward Slave Strut
The original upper aileron drive had the slave strut attached to the ailerons behind the hinge line. Early on, several incidents of aileron flutter were experienced. These were determined to be induced by a combination of backlash, lack of aileron system balance, and aerodynamic oscillation of the streamlined tubing slave struts in these specific constructions. The aileron system was redesigned to make it a lot more tolerant to play and imbalance by moving the slave strut attach points forward of the hinge line, thus the term "forward slave strut". It was also recommended that round tubing be used for the slave struts, or a spoiler ridge be added on one side if streamlined tubing is used, to prevent any periodic aerodynamic oscillations.
Landing Gear Geometry
The original Skybolt gear geometry was much lower with the wheels forward from the current location. This made full-stall landings impossible, and the forward cantilever component of the wheel position placed excessive torsion loads on the hinge bolts during hard landings. The wheels were moved aft, and the hinge bolts up-sized from 3/8 to 5/16. The new gear had superb ground handling characteristics. There is an easy way to tell if a particular Skybolt has the original gear (it is rare these days). If you are 5'10" or so, the spinner will be at chest level. With the new gear, it will be at nose level.
Another change to the gear was to up-size the wall thickness of the shock cord truss to .049. There had been instances of significant damage to the truss cross-member by the stop cables on very hard landings. Repeated dimpling and crushing of the cross tube by the stop cables eventually caused several truss failures.
To satisfy the 6-cylinder weight and balance envelope, the fuselage was extended three inches. The current fuselage length is 168 inches from firewall to tailpost.
We rarely see examples of these early features. Most of the existing Skybolt fleet has been modified and upgraded.