Finally got those TS Cutter edited files playing on the 360..
1)
h264TS Cutter - As has been posted, in Options/Settings/Advanced, change CutIn frame type to I-Frame, and CutOut to All-Frames. Don't forget to use the scrollwheel, makes the editing process a lot easier. Cuts aren't 'frame accurate', but they're pretty close. **Update** Also in Options/Settings/TS-Settings, uncheck Sync Audio/Video Delay, otherwise you'll get sync issues that get worse at each cut point.
2)
tsMuxeR - No settings to change, just add your edited ts file, click Demux, Start, and wait. You'll get a .264 file and one without an extension, make the latter .aac.
3)
mp4Muxer - Click Add, and add the .264 and .aac files (separately). Above the Add button, click Browse and name your output file. Only setting to change is the FPS, set it to 59.9401. In the upper left corner of the window click Multiplex.
That's it, you should have a file playable (streamed or otherwise) on the 360 in all its HD glory..
Couple of notes... and where I got hung up..
* When editing in h264TS Cutter, if you remove anything from the beginning, it won't play on the 360. So you need to keep at least one frame from the beginning of the file. To do this, make sure the Start box is at 0, click the > button once to move ahead one frame, and click Add. Then go on about the rest of your cuts as usual.
* The 360 will not play files over 4GB in size (except for wmv). If need be, you can set h264TS Cutter to split its output in Options/Settings/TS-Settings and then demux/remux them individually as explained above. Ideally, you could just split the final mp4 file, but I don't think it can be done. I'd recommend figuring out the bitrate you need ahead of time, as opposed to using the max 13.5 or even the default. I captured the same piece of video at 13.5MB/s and 5MB/s, and reencoded the 13.5 down to 5 (same format), and there was no comparison, the lower bitrate video encoded by the HDPVR was FAR superior.
Hope that helps somebody!