Curious...why did you create a custom sequence for your 720p60 footage? There is a standard preset for AVCHD 720p60 that works great.
As for MPEG output options, you probably are limited to 50i (PAL) which would be 25fps or 60i (NTSC) which would be 29.97fps. The 60i output should work fine for 60p source footage. However, I haven't got a clue what custom settings you made in your custom sequence so that could be botching up the whole operation.
As for "best export settings" and other recommendations, this is the general workflow (not 100% universal, but pretty close for most editors). Sequence format is dictated by source footage. If you have mixed formats or framerates, then you can just use a sequence preset that most closely matches the majority of the clips. Then you do your final formatting based on the destination of the file. So you'd export a file that is compliant with whatever display technology you are using (web, TV, etc) and standards (NTSC, PAL, YouTube, Vimeo, etc).
So yes, MPEG2 TS with 720p60 footage means you probably want to do 480i (29.97)
Hope that helps!
