I have a different brand, but the manufacturer specified the primary loop pump speed based on the max output level...you do not want to increase it beyond that. High flow can cause cavitation and erosion of the pipes and boiler heat exchanger. You'd know if it was too slow, it would likely start to get some flashing to steam, and would be very noisy.
You want the temp to be as low as possible, while still heating the house adequately. If it cycles too much, or short cycles, you may need to look into a way to add some mass. The delta between high/low may have changed. If that's too small, it will cycle more.
There's generally no big reason to oversize a boiler to run an indirect. The only reason I can think of is if you use hot water continuously, like say in a spa or commercial laundry. Otherwise, it generally runs as a primary zone, and gets all it needs, and in your case, that's over twice a typical stand-alone gas WH burner would have...so, it heats much faster, and the system can return to heating the house before you'd notice.