My vehicle was designed with a 55 tooth tone ring in mind for the ABS system. I am currently in the process of starting a axle swap which runs a 52 tooth, Changing the tooth count would be a long and expensive and complicated process.

Would the ECU throw a fit over missing 3 teeth? Is it possible to adjust the tune for this 3 tooth difference?

 

Depending on what vehicle it is and engine tranny were talking here. Chevy stuff has speedo ran off of the VSS on the tranny. The tone rings are solely for wheel speed off left and right rear wheels. Having less teeth I think would speed up what the abs unit is seeing for wheel speed. So if theres much over a 3-5 mph difference front to rear it will aggarvate it and also effect traction control operation if say you are working on a F body with 4 channel abs and traction control.
There is no tuning on the ABS unit to tweak things. you are in that gray area of gotta try see how it reacts and then formulate next steps from there

 

Yeah, you need to tell us what year and model vehicle this is. If its an older vehicle with only ABS and no Stability control, then I don't think the small tooth count change would matter.
However, if its a newer vehicle with Stability control, then it might throw codes and even limit acceleration.
For example, the 2006 Corvette I had came with staggered tires sizes front and back; when I installed equal size track tires, maybe 5% smaller at back, the Stability control went crazy and put the car into limp mode. Fortunately I could turn it all off.

 

It is a 2009 H3 running a E67 ECU, The front wheels could be adapted to run 55 tooth at quite the cost, however the rear Tone rings could be replaced with 52 tooth tone rings. Would the system care if both axles are running the same wrong tooth count?

 

Doing a little more thinking, moving the rear wheel reluctors to 52 tooth might work, as the ECU doesn't know a set point like with the reluctor on the crank, it just knows the rate something is spinning at, and with less teeth it'd just know that everything is spinning slower, now the ECU might compare this speed to the transmission output speed which might cause issues at higher rpms where the expected wheel speed difference will get bigger and bigger, but I don't know if it cares. Now this out of spec wheel speed issue would also be caused by changing the gear ratio of the differential too