You can use the skipfirst= and back= options in the ESTIMATE statement to control the span of measurements used for parameter estimation (ESTIMATION SPAN). The (one-step-ahead) residual diagnostics (such as ACF and PACF plots) are based on the ESTIMATION span. Similarly the skipfirst= and back= options in the FORECAST statement control the span of measurements used for producing forecasts. Miultistep-ahead-forecasts are produced based on the end of forecast span. I do not know R implementation of the UCM models and cannot comment. I think the UCM doc is reasonably complete and explains the meaning of all component estimates (filtered and smoothed) as well as the residual diagnostics.
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