I have a new Peerless, Tankless, hotwater boiler.
The bathroom is next to the boiler so the piping is very short.
The shower starts hot then goes to cold and gradually becomes hot again. I have to let the shower run for a while before I get consistent hot water.
What is the proper settings for the controller. How should the hi limit be set compared to the low limit.

Before you check the settings of the unit take a look at your gas supply. Many of the units sold require a higher gas pressure then utilities normally supply. Most utilities supply 6.5"wc standard pressure. Many instantaneous water heaters need up to a minimum of 10"wc to preform properly.
The minimum pressure will be listed on the side of the unit and you can call your gas supplier for their delivery pressure.

My boiler is oil fired