Rinnai R53 Natural Gas Tankless Water Heaters

now to me this would result form not enough water going into the system. do you have a seprate unit on the bottem to take off and clean?

It sounds like the Rinnai units are working correctly but you've got some plumbing problems.  Any tankless heater has a minimum water flow required to keep the burners going.  If the burners were going with very little water flowing through them to carry the heat away, the heat exchanger could overheat and fail.  The solution is generally to the electronic controls to set the desired temperature and then just use hot water.  Once you start mixing cold water in, you actually reduce the flow of hot water and the burners turn off.  If you are right near the cut off point, the burners will cycle on and off resulting in those very annoying hot-cold-hot-cold showers.  
The fact that you've got those very loud noises indicates some other sort of plumbing problem.  Hooking up two tankless units in series is much more complicated. In heavy draw situations, the second unit is asked to finish heating the water up to temperature when the first unit couldn't quite get it there. Now you're putting hot water into a heater and heating it more.  You have a lot more issues with fluctuating temperatures and pressures within the pipes which could conceivable cause these horrible noises.  Everything's got to be set up right to for things to function properly and it's easy to get something wrong.
From your description, it sounds like a better solution would have been to mount the two heaters in different places. e.g. One in the basement to serve basement and first floor faucets.  The other on the second or third floor to serve those two floors.  Since these units are direct vent (don't use inside air), they can even be mounted in a closed closet as long as the vent can get to the outside.  With this setup you avoid the complexities of a series installation and you also have a much shorter wait time (and therefore less waste) for the fixtures on the upper floors. 

FWIW, the most common problem with tankless water heaters is under-sized gas piping - they need a LOT of gas RIGHT NOW. They do use less in the long run, though.

Another common problem is incorrect venting. A cross-connection between hot & cold water piping will also screw things up.

The best people to talk to about it is the manufacturer. If the heaters are new, they're under warranty - you should take advantage of that.

I have the same problem from time to time, adn I concluded it's a water pressure issue. I solve the problem by running hot water through as many pipes as possible to stabolize the pressure. I havne't figured out a fix yet, but I think it's a water piping issue.