I see that speed is everything with landing this baby.  A few knots too many on a manual landing and you're halfway down the runway at touchdown!
I look at it this way. When looking at the 777 from the left or right side in Locked Spot view, make sure that the nose wheel is above the main landing gear (nose up attitude). That way the landing will be softer. as I said before, it does flare, but it is not very much. Sometimes, it doesn't flare at all! And the landing is going to be pretty heavy. This might be what you are seeing.

I flew this plane most of the day yesterday.  It is great when ity all goes smoothly, but I have some weird things that happen.
Mine flies very well most of the time - about 90% or better.

According to Jon M's tutorial, when I put 250 into the speed window on the MCP,  the VNAV logic in the CDU is supposed to honor that restriction until I get to 10000feet.  On my first few flights, this seemed to work, but the last few, it can't seem to manage it.  More like 270.  Maybe it is running out of elevator authority.
The VNAV should honour the speed you enter in the Speed Indicator. I assume that you are clicking in the centre of the IAS/MACH Selector so that VNAV is still active, but you are controlling the speed.

The CDU also changes all my speeds in the Legs page to 315 after takeoff.  I was flying from Chicago to St Louis at fl280, and several of the legs were displayed as ".80/280" in the Legs page after CDU programming was complete.   But they all changed speed to 315 by themselves.   So then when I get to altitude, I have to do your left-click on the speed knob trick to get a cruise speed of .80.
Strange. I haven't seen that myself. I can't think why it would change them. Next time that happens, check the VNAV CRZ page (page 2/3), and see what is entered in there for the speed. If it show 315, change it to 280 and the wspeed on the waypoints should change to match it.

Also, somehow now my marker beacon audio is sounding on takeoff.  Where are the controls for the audio for marker beacons?  
I can only assume that you are overflying some marker beacons after taking off, so they are triggering the sound. I have had this happen in other aircraft before (which possibly includes the Cs7770, I just ignore it.

If I want to do FLCH mode to climb instead of VNAV, will the thrust settings for climb still change from Takeoff to Climb automatically?  Or do I have to do that manually?
As far as I know, it will change on it's own. I rarely use FLCH, mostly VNAV, but that because it works fine for me almost all the time, as I said above. I gave the 777 a good run of tests out of Heathrow (EGLL) where a lot of time is spent holding altitude due to Altitude Constraints in the SID's (i.e. 6000 feet in the SID DVR6K), and even though I had entered the Cruise Altitude in the Altitude Indicator, it stopped at, and held, 6000 feet until it passed the waypoint that allowed it to continue the climb. So VNAV is working really well for me.