  The CO Mapping Array Project (COMAP) Pathfinder is performing line intensity
mapping of CO emission to trace the distribution of unresolved galaxies at
redshift $z \sim 3$. 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 available for high-level
analysis is a factor of 8 higher than in ES. The resulting maps have reached an
uncertainty of $25$-$50\,\mu K$ per voxel, providing by far the strongest
constraints on cosmological CO line emission published to date.
