So if I leave the marlin accel values alone since I think they are high anyway (can I check in RH M code what they are?)
Can I just set in slicr advanced and be done with it?

How do I run the program? DO I load it into marlin or run standalone and connect to the printer directly? i do not see an exe or dmg file

Its a QT program.. so you have to 'compile' it (on Linux, or Windows..) ... and it runs standalone and connects to the printer directly.  But hey, no love lost if thats a bit complicated - was just a suggestion for having a repeatable and automated method for determining the maximum acceleration you can achieve... by no means neccesary (you would note in that image that the program does exactly what you are after - but in that case he was testing for highest speed with 10000 as the acceleration vector, so he was testing it in terms of keeping highest accel with best speed rather than reducing accel to get higher speeds... But basically it keeps upping the acceleartion/speed value by a set value and keeps running the test until it fails... and then you know your highest acceleration/speed is the value used before the failed test ..) .. It just makes it easier for us lazy people

You can do it all by hand yourself in G-Code.. just write a big text file and paste it in to RH... Use the G-Code EEPROM adjustment commands to adjust the acceleration between each iteration, and you can then use a set of define movements (say full strokes in both directions, then half strokes, then a diagonal) to test the performance. Then you can just cut-n-paste that set of g-code numerous times and just adjust the G-Code line for the acceleration vectors.

Yes I realize the difference between servo/stepper just used servo easier. Steppers have there place though. For fixed position movement back fourth to specific points, and high torque applications (vs cost) the steppers are better then servos. if continuous motion and positioning are critical then servos are better.

Documentation is pretty light on.. but its basically a program you run and connect to your printer. It then allows various Temp PID tuning and Acceleration tuning ...
Its development stalled back in 2011, but its still valuable as a tool with what it developed to date...

Just an FYI too, they aren't servos - they are stepper motors which is very different. (they don't have integrated feedback - a servo is very different to a stepper due to its feedback capabilities through a pot or other encoder (if dealing with continous rotation servos..))

And FYI - Steppers are meant to 'sing' even when being driven perfectly - the sound isn't necessarily reflective of performance other than if you hear ticking noises.... for exmple these motors aren't being abused (much) at all..

So far it is much more improved and my litmus test is the sound. I know all is great when I hear a nice mild humming of the servos with the extruder fan running. If i hear some clunking of the extruder head or popping of the carriage I know I am getting some slip or bind. I still have that in some areas but I suspect it is the loose linear bearings now slipping. next project will be to reprint the y slides and drill hols so I can twist tie the bearings in place.

what is qt-marlin? I will read the link. running at 120% and the overshoot loaded up the Y current setting for sure. I have a Surestepper driver and I know it will do 2amps safely but I have it set at the default SD setting. I am going to tweak it up 10-20% and see if that helps with increased speed as-is.

I have a extra servo that is higher current torque load then the Y SD one. I could swap that one in if all else fails and put the Y servo on the X since it is bigger as well.

No pillow block, I have all the parts but the shaft is so rough even with dremel sanding it was so hard to get the bearing on that far without binding on the rod. And all the pulleys are for 6mm dia rod, which the rod is, but the gt2 upgrades are only in 5mm. I can find 6mm rod but no 5mm precision rod to replace it with. So until I get a 5mm rod i will not add pillow block.

I did add flanged bearings in place of the bushings in the back y rod and that made a huge difference and to me more important then the pillow block. It is 2 points instead of 1 for the pillow block setup and they are closer to each pulley which is more critical for loads

I did print the front pulley blocks as well but they look so complicated and hold the rod as well, I might reprint smaller ones that just strengthen the support and allow 5mm flanged bearings as well. One comment here. is the pulleys on the idlers are not grubbed to the bolt. they spin freely so bearings on this are not going to do much unless the idler is fixed to the bolt

I would like to see an x carriage with ability to add a flanged bearing/rod setup for the right side idler as well then you can crank the tension up too and eliminate some torque needed for the small x motor

A couple of things here.
1. Don't under estimate the value of the pillow block.  Pull that rod out and spin it with a drill use some emery cloth to turn it down till your bearings fit.  This only needs to be done on the first couple of inches.  I have six bearings on mine (overkill I know).  two replacing the bushings in the case and two pillow blocks (two bearings each) on each side.  I absolutely couldn't believe the huge difference it made.  Especially the one on the left side.
2. I have bearings on my front idlers and used a set screw to secure it to the bolt (don't tighten the bolts too much).  Now those bolts spin with the idler pulley.  If I remove the Y-Drive belt to the motor the movement is so smooth that a strong breeze will move it back and forth.

so i know tension should not be an issue now. I have both belts tight now. i do hear more noise in the y I suspect when the head moves at x-y angels. I think belt tension and torque. so maybe a little too tight  but the circles seem spot on and repeatable layer to layer very crisp resolution even at .28 layer height.

The X carriage mods on here is good but the x carriage part is a little thin and doesn't align well. i found a better design all-in one on thingiverse which feels solid and takes out all slop on the bearings BUT it doesn't have the 2 belt tension screw holes. Weird? So I having a hard time getting the belt mounted ot the x now. It is not aligned from front to back so the right side is about 1/2" taller then the servo side on the X. so I think i am getting extra torque and loading. I need to design a belt holder that I can mount to the single screw hole on the x carriage that will fix  1 side and still allow adjustment for the other side.

Check out http://calculator.josefprusa.cz/ and the last calculator to get a feel for how different vectors effect how you accelerate and decelerate over various distances...

Anyway - if you feel theres something to be found:
Slic3r Advanced acceleration values sets the GCode generated acceleration vectors when in the various print modes.
RH's EEPROM Acceleration values impact the Firmwares max values - the firmware will not process movements using values above those vectors and will keep them constrained to those values (i.e, it is the 'cap'...).

In short - You could put what you want in Slic3r, but it will always be trimmed/capped by EEPROM...
Except for the few places where that all goes out the window inside Marlin... but these tend to be limited to edge cases.

One suggestion as well is to spend some time with QT-Marlin if you want to play with acceleration vectors.. it will require you to rig a full set of end-stops though, as it detects the acceleration success/fail by measuring missed steps across a known distance between two end-stops in both directions.. but it at least takes the heavy lifting work out of trying to arrive at reasonable figures.

I did add flanged bearings in place of the bushings in the back y rod and that made a huge difference and to me more important then the pillow block. It is 2 points instead of 1 for the pillow block setup and they are closer to each pulley which is more critical for loads

I did print the front pulley blocks as well but they look so complicated and hold the rod as well, I might reprint smaller ones that just strengthen the support and allow 5mm flanged bearings as well. One comment here. is the pulleys on the idlers are not grubbed to the bolt. they spin freely so bearings on this are not going to do much unless the idler is fixed to the bolt

I would like to see an x carriage with ability to add a flanged bearing/rod setup for the right side idler as well then you can crank the tension up too and eliminate some torque needed for the small x motor

So I know I want to play with my accel values. Maybe be safe at first and make sure I am runnnign ok at base speed then crank speed up first, then accel.

But I see so many accel values in Marlin, In Reptier and in Slicr3 I am not sure what is the true accel for x-y-z.

Slicer has values for accel, but when I load a print I see different values from Marlin in reptier. And the values in Reptier do not seem to match the ones in Marlin

so where is the best place to set default accel that overides all.