Does Mesa 5I24-25 would work on PCIe 2.0 x16

Sorry for making confusion for velocity encoder it is exactly what you said " using motor encoders to close a velocity loop and then digital scales for position, in which case you have the count correct."
I will get motor encoder count from drive as drive have functionality to provide it and will attach 4 linear encoder and on rotary encoder for positions feedback.

Well I have bought a Dell optiplex 7010 with i5 3rd gen(originally paln to use with ethernet based board 7i80hd-25 which is unavailable right now)  but I don't have any issues with what size of chassis it have coz like you said I have planed to take out mother board and install it in cabinet

But i have confused if I have to bought 5i24-25 which is PCI and pc I want to use is having PCIE only so and 6i24 also not available so using pci to PCIE adaptor will affect perfomance? 

If you can find a PCI motherboard, that might be simpler.

But if it is all going to be sitting in a control cabinet so space isn't a problem, then you can try the adaptor. It should work, but I have had experience of a PCI to PCI right-angle adaptor that prevented the machine booting, and that was just changing the angle...

That's what i am afraid of using such adopter may cause performance issue luckily i find a mother board that supports PCI as well I5 3rd Gen processor now as you mentioned i have make it simple. Thank you.