While removing the transmission might seem like it would give you more space, the added complexity and work involved in removing, reinstalling, and re-aligning the transmission often outweighs the benefit. Leaving the transmission in place usually allows for more convenient access to the engine mounts and other critical components. You'll likely have to unbolt and carefully maneuver the engine, but this is often a less labor-intensive process than full transmission removal.
However, this depends on your skill and tools. If you're very experienced and have the right equipment, removing the transmission *might* be slightly faster in your particular situation, but for most mechanics, keeping the transmission in place is the preferred and less error-prone method.
