Ok, I'll try walk you through one of the typical timeout situations. You settling parameters here told PHD2 that you wanted star deflections to be less than 1.5px for 10 seconds and you didn't want the entire dither operation to take longer than 40 seconds. Here's what that looked like:

Point #1 is the start of the dither operation at 03:23:48. It requests a large dither in both RA and Dec, meaning that the lock-point is "instantly" moved by 9.7 px in RA and 7.4 px in Dec. This triggers two large initial guide commands that attempt to move the guide star quickly toward that position. Because you are trying to run with a poor calibration, these initial guide pulses took 8.2 seconds in RA and 2.9 sec in Dec - the poor calibration is why the RA guide pulse is so large. The initial RA correction resulted in a large over-correction, which then triggered 6 successive RA guide commands to restore order. The first 5 of these specified a guide pulse of 2.5 sec. By the time all of this was completed, you had burned through 35 seconds of elapsed time, leaving only 5 seconds left before the timeout limit. But your settling parameters said that you wanted 10 seconds of guiding with less than 1.5 pixels, so you were simply out of time and triggered the timeout.
Going back to root causes, you got a "poor" calibration result which you didn't do anything about. The reported guide speed in the mount is 0.9x sidereal which is 13.5 arc-sec/sec. That part is fine. But the measured rate of west RA movement seen during calibration was only 6.1 arc-sec/sec, less than 1/2 of what it should have been. And this is why these large dithers that require large west guide corrections take so long. Smaller dithers that need only east corrections generally settle quickly. Are you sure the payload is well-balanced in RA on both sides of the pier? It looks to me like it might not be because the response to west guide commands is poor when the scope is on the east side of the pier.
In order to work through these problems, you should learn to use the LogViewer tool and do as I have done here - zoom in to see the gory details of how the mount is responding during these dither and settling periods. It can be a time-consuming process so it's not something I can do for you on an ongoing basis.
Good luck,
Bruce