An engine that runs roughly can have a leak at the valves. An engine that runs roughly can also have valves that need an adjustment. Remove the head and inspect the valves and valve seats. This action is necessary to find those small defects that would not normally cause problems. Repairs of these problems are normally performed when you are reconditioning the engine.
This Caterpillar engine uses Keystone piston rings. Keystone piston rings are designed to expand during the compression stroke of the engine. At engine cranking speed, the Keystone piston rings do not fully expand. This results in unstable readings for cylinder compression. As a result Caterpillar does not recommend performing compression tests on engines that use Keystone piston rings.