Was the engine purchased as a crate (all assembled) engine or was it assembled by an engine shop? Most crate engines are quite good these days. If the engine runs with no vibration outside of the 2000 ~ 2500 RPM range then it's likely mechanically OK. The old damper is of some concern. I would look into the damper/flywheel comb for peace of mind. Not vibrating on deceleration suggests that it's not an engine balance issue but that's not conclusive.
CV joints are typically much smoother than U-joints and tolerate higher shaft angles much better. CV joints are superior to U-joints. Practically every car today with axle joints uses CV joints, certainly every high end sports car and every race car does. A half shaft issue/vibration would most likely be related to vehicle speed not engine speed. I don't know your setup but I know Scott does nice work. Personally, I would not go back to U-joints. Most likely not your problem if they are installed correctly.
Can you better describe the vibration. An engine imbalance can feel different than a fuel-ignition induced rapid misfire kind of vibration.