Rinnai r94ls seems to stop heating heating water to certain faucets

SOURCE: Rinnai R53 Natural Gas Tankless Water Heaters

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. 

SOURCE: rinnai unit

OK, sounds like a sensor problem to me. The temperature reading is done on the backside of this unit. Remove the top cover and with a flashlight in hand, look for a small black rubber probe with yellow wires attached. You will find it about 2 inches above the floor and on the right hand side (when viewing from the front). Make sure this probe is not being influenced by the venting system and showing a “false” reading. If the vent pipe (the one covered by cloth) is close to it, the probe is made that you can relocate it out of the way of the vent. You will need to get to both the backside of the heater and go inside the heater cabinet to do this properly. If the vent is a few inches away and not influencing the probe, place a cold cloth on the probe and see if the temperature drops. Then a warm clothe on it to see if it rises. You could have a bad probe. List your model number and I can get you a part number.

SOURCE: Rinnai 1004 heats to a temp 4 degrees higher than set temp, adjustment?

You can adjust the position of the room air sensor found on the back of the unit between the heater and the wall. It is a black rubber bulb with yellow wires. There is a few inches of extra wire you can extend higher to get a more accurate reading of room air. While you are back there, check for drafts that will give you false readings.

SOURCE: my rinnai water heater keeps cutting off while

Sounds like a bad flow switch.

SOURCE: have a 1004fa model to heat a room. temp on

You may have a bad circuit board. Depending upon the age of the heater it may still be under warranty. Contact Rinnai (in US) 800-621-9419 with your serial number and installation date. Ask if they can offer a solution. Good Luck!