Just a few thoughts / comments.
Variable reluctance sensors' voltage changes with speed, low V at low speed, high V at high speed. The voltage can vary by a factor of 100 over a normal RPM range. Also, the voltage swings positive and negative. You can't connect a VR sensor to a micro with a simple resistor divider.
I question the tachometer circuit. It's output will be a signal between 0 and 15V, either a pulse width modulated signal or an analog voltage (depending on filtering). I think the VR signal conditioner on the front end needs some protection and it may not work at slow speeds. I don't understand what the block labeled "charge pump" does unless it is a switched cap amplifier to isolate the output from the input.
You really need to put an oscilloscope on the signal and see what you have to work with. What is the signal going to the tachometer in the cabin? Does it get the raw VR signal? or is it processed somehow? Can you capture that signal?. In the end it may be easier to add another sensor to the engine. Most Hall effect sensors or optical sensors put out simple digital signals that can be connected directly to a micro. You may be able to select the number of pulses per revolution to something that suits your system better.
Speed and throttle don't usually change very fast in a boat; if you are logging hours at each speed / load you probably don't need millisecond data. Why not measure one input at a time (particularly the fast engine speed signals) and then send the serial data all at once. Measure engine 1 for 100mS (or whatever makes sense) then measure engine 2, then measure the flow sensors. Then send one message with all the data. Alternatively send the engine 1 message while you are measuring engine 2. By the time you are done measuring engine 2 the first serial message will be complete.
You should be able to capture a set of data every second or two which is probably good enough for an application like this (if I understand it correctly)