Jamming of Y axis.

I had a ton of problems with y working than not working what solved it for me was to not use the supplied grease
and used silicon spray instead.

...
I've thought this was an alignment issue so using my ruler I made sure that bothe sides of the gantry were equal. Also Rory, who has been very helpful in the past, has said it could be that I need to tighten or loosen the adjustment screws so everything slides smoothly. I have re greased, tightened, loosened, taken apart and put back together as well as leveled the machine. The only thing that has seemed to make a difference is to slow the whole machine down in the Y parameters menu in the program UCCNC. Because I am completely new at this stuff I'm unsure which one to slow down. I've changed homing speed up and down, steps per unit,velocity and exceleration. I don't know which one is actually making the machine slow down in between pieces!

Could someone please help to shed some light on the problem? Yes it would be nice to have the machine run smooth at any speed perhaps I'm an idiot and have put it together completely wrong. ( This could be the case) But I thought there would be a manual that would explain what all the perameter meanings are in the program UCCNC. What does what? I've searched. Am I missing something?

A ruler might be too inaccurate for aligning the gantry. You could check following two topics:
https://www.stepcraft-systems.com/en/forum/assembly-and-maintenance/1741-y-axis-loosing-steps

https://www.stepcraft-systems.com/en/forum/operation/2362-tracking-wrong
It is important how you tighten the screws. Some information in the referred topics could be SC v1 specific.

you should be able to move a well setup STEPCRAFT machine at 4000-5000mm/min rapid rate with smooth performance on all axes.

Where does the issue happen? Towards each end? or in the middle?

It seems to be all over but only when the machine wants to moove fast.

disassemble and retune following the video steps. You should be able to run the machine at 4000mm/min for tests

I also have issues when the temperature drops below 60F. Something is binding below that temperature.

I was having a similar issue. Drove me nuts for two weeks. X and Z axes were fine once adjusting the rails but for the life of me I couldn't get the y-axis to reliably traverse. Skipping steps, jamming, binding... Alignments, rail adjustments, tensioning... Nothing worked.

Finally figured it out. The lock nut on the left side screw pulley was too tight. Was causing notchiness in the bearing and random binding. Backed it off a little bit and it was all free and smooth as silk. Realigned things, ran end to end traversals at 100% speed. All good now.

I was also having this issue, tried to avoid a disassemble but that's what it needed. From what I can tell
my problem was the lead-screws were not centered to the end bearings and I had overtightened the pulley lock nuts and too much tension on the belt.