I've been saving these up in an effort to not completely spam the forum.  Let me know if there are settings I can tweak or if I just have to "suck it up" and adapt.
 
#1.  Playback now-time scrolling is jerky in track view.  Is this a video issue?  It doesn't look real smooth and tends to get "stuck" briefly and jump forward at times.  This is not the PAUSE button it's just not as smooth as it was in 8.5 (on a different computer with a different video card).
 
#2.  When I'm working with video and have the video view selected, I inset a marker and the focus goes back to track view.  I don't want to have to click back over to the video.  I like to use <-- and --> to shuffle the video forward and back and insert markers as needed.  At least that's how I did it in 8.5.  Having carpal tunnel and repetitive stress injury in both hands, the keyboard is very important to me I don't like to have to touch the mouse.
 
[SOLVED] #3.  When I export audio there used to be a status bar on the bottom of the screen so I could monitor the progress.  Is there a way to get this back?  This is especially handy exporting a 5+ minute chunk of audio.  Yes it only takes 5-10 seconds, but every time I see nothing happening except the blue spinning wheel I instinctually panic.
 
[SOLVED] #4a.  I don't mind this new "smart" tool that lets you move and select and whatnot... but when I lasso PART of a clip I want it to select the ENTIRE clip, is there a way to do this? I want my lasso back!
 
#4b.  Not quite as important but I wish the window would remember my preference of tool. For example I will always want the "smart" tool in the track view but when I go to the piano roll I will always want the "select" tool. I have them set to key bindings but still... 8.5 kept the tool choices separate.
 
[SOLVED] #5.  In 8.5 I had my MSR buttons to the right of the volume/pan which I liked. In bike terms we'd say this was an aftermarket modification but I don't remember how I did it. Is there a 3rd-party patch or utility for this in X3?
 
#6.  Can you seriously not select a track by clicking on the NAME of the track? Just seems so counterintuitive to me. Guess I will get used to it eventually. Why would they change this?
 
[SOLVED] #7.  Scrolling in piano view... I like to edit in real time, watch a performance go by and delete any small mistakes as they scroll by. I click on a midi clip, it opens the piano roll, the piano roll is scrolling properly but as soon as I delete a note it stops scrolling and "sticks" where my edit was... is there a setting for this?
 
[SOLVED] #8.  When I split a clip like this:

I expect this to happen:

Not this:

Is there a way to change this?
 
Thank you in advance for any help it is truly appreciated.
　
 

Personally, I would prefer seeing a pile of individual posts vs. a "laundry list"; it makes it easier to give and track the responses to specific issues. Anyway, here are a few:
 
- Jerky Now time; Try disabling Aim Assist or setting snap resolution at a higher level. Some have reported the problem generally, but I'm only seeing it with Aim Assist on and snap off or at a fine resolution.
 
- Bounce/export processing status is now shown in the transport module's display.
 
- Lasso with right-click will select entire clips.
 
- MSR buttons display to the right of (or below, depending on track pane size) the track Name field in both 8.5 and the X-series for me. I'm not aware that this was ever customizable. Maybe Panup's mods allowed it...?
 
- Never really noticed that clicking on the track name no longer changes focus. I only ever clicked there when I wanted to rename the track. But, no that does not work the same way in X3 as it did in 8.5 and X1. Appears to have changed with X2.
 
- See Options > Click Behavior in the Track View menu to disable Left Click Locks Scroll. Or click in the timeline to restart scrolling. 

Brilliant!!  Thanks!  MSR buttons definitely involved editing some sort of INS or INI file I just don't remember where.  I will try google more...

#9.  I turn auto crossfade on/off a lot.  I have it set to keybinding "X" not sure if that's standard or something I did.  I used to have a visual reference I could quickly glance and see if auto crossfade was on or off before I moved a clip.  Is there any way to see this anymore?  Aside from clicking on the options menu? 

5 - does alt-drag on the widgets not move them still? I'm pretty sure I've rearranged my track view widgets in X3!

Yes, it does. I was not aware of that feature.

Yes!  And that is much easier than the way I did it last time...

Matt
#9.  I turn auto crossfade on/off a lot.  I have it set to keybinding "X" not sure if that's standard or something I did.  I used to have a visual reference I could quickly glance and see if auto crossfade was on or off before I moved a clip.  Is there any way to see this anymore?  Aside from clicking on the options menu? 

This is a common complaint about the X series, and I'm pretty sure a number of feature requests have been entered about it.

Not an immediate answer, but I just thought I would suggest perusing the Groove 3 (and other) tutorials to keep up to speed on ever-changing Sonar.
 
As I progressed up the ladder of Sonar versions I found changes were just too much for me figure out each time I ran into one, so I broke down and got into the Groove 3 Sonar videos.  I actually learned about the many choke points I had just been blundering through.  I also learned better ways of doing things I thought I had already mastered.

#8 may be due to having Non-Destructive MIDI Editing option ticked.