Hi,
Welcome aboard!
1. I don't know how you have your project set up but normally the entire skeleton would be in a single Bones layer, so you would select all the bones for the walk cycle, and then use Alt to stretch or compress the range between the selected keys. The key is to make sure you have keyframes at the beginning and end of the cycle for all the bones related to the cycle animation (i.e., legs, torso, and arms.)
If you have the Bones in multiple Bones layers for some reason, you'll need to select those layers as well (you can use Timeline Visibilty for that.) I highly recommend keeping everything in a single Bones layer though. (To me, creating multiple bones layers for a single character sounds like a nightmare to animate.)
2. Again, this depends on how you've set up your project.
Render times can vary depending on the complexity of the rig and artwork, the resolution of any bitmap images, the number of mesh warps in use, etc.,. Optimizing the artwork and rig complexity can speed things up.
You can also reduce render times by disabling Extra Smooth images. This option basically renders the frame at double the resolution and then scales it down to the target res to improve the AA quality, but obviously this can increase the total render time by 4 times. Disabling this option can dramatically speed up the render but potentially at the expense of quality. (Give it a try. Depending on your design, the difference in quality might not be noticeable.)
Somewhat related...
I always render for compositing so I make use of Moho's Layer comps system. This means breaking out multiple passes for bg, mg, fg, character and probably fx. (Sometimes I'll also render custom matte elements for compositing effects I can't do in Moho.) For any static layers, probably like backgrounds, I'll only render a single frame or simply add the original art in comp. Since BGs can take the longest time to render in Moho, this eliminate that time from my Moho renders. Using Moho Exporter instead of the Export Animation command allows me to batch process all these passes with a single mouse-click.
I also always render to image sequence (from any animation package, not just Moho) because this is faster and more reliable than rendering directly to a movie file. I can always render my movie file later from my composting and/or video editing program.
Now, collectively, this process can potentially take longer but the pay off come after I've composited the scene (i.e., in After Effects, Nuke or Fusion Studio,) because when I need to update something in the animation, I only need to update and re-render the changed Layer Comp and affected frame range. The difference in render times can mean a few seconds to a few minutes for the revised layer/range v.s the time it takes to render the fully composited file from Moho.
Rendering the final composite from Ae, Nuke or Fusion can go more quickly because those programs don't need to process the rig deformations...that work has already been taken care of by Moho.
This is more or less the standard workflow I've used at every studio I've worked at or in my own personal projects. It's a very efficient workflow, especially when I need to quickly respond to notes or to make my own changes.
3. You can move the
layers in 3D but you can't lift the points from the layer's 2D plane along its z-axis to create 3D topology. When you see moho artwork animating in '3D', it's usually being deformed along 2D plane to look that way using Moho's mesh warping features along with Magnet and the other deformer tools.
I use these method to fake 3D animation all the time in Moho. For an example, watch the '3d' truck in this clip:
Car Chase from Boss Baby. This truck is actually entirely 2D, and it was rigged and animated using Moho (along with the truck driver, Timmy and Boss of course.)
Yes, this is cheating but it's all about getting the desired final result.
Hope info this helps.