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The CO Mapping Array Project (COMAP) Pathfinder is performing line intensity mapping of CO emission to trace the distribution of unresolved galaxies at redshift . We present an improved version of the COMAP data processing pipeline and apply this to the first two seasons of observations. This analysis improves on the COMAP Early Science (ES) results in several key aspects. On the observational side, all second season scans were made in constant-elevation mode, after noting that the previous Lissajous scans were associated with increased systematic errors; those scans accounted for 50% of the total Season 1 data volume. Secondly, all new observations were restricted to an elevation range of 35-65 degrees, to minimize sidelobe ground pickup. On the data processing side, more effective data cleaning in both the time- and map-domain has allowed us to eliminate all data-driven power spectrum-based cuts. This increases the overall data retention and reduces the risk of signal subtraction bias. On the other hand, due to the increased sensitivity, two new pointing-correlated systematic errors have emerged, and we introduce a new map-domain PCA filter to suppress these. Subtracting only 5 out of 256 PCA modes, we find that the standard deviation of the cleaned maps decreases by 67% on large angular scales, and after applying this filter, the maps appear consistent with instrumental noise. Combining all these improvements, we find that each hour of raw Season 2 observations yields on average 3.2 times more cleaned data compared to ES analysis. Combining this with the increase in raw observational hours, the effective amount of data …