John, As Roy and Russell have mentioned, you do need to use a depthing tool to plant those pivot holes. forget marking the centres out any other way,
I'd also start from the centre wheel and work outwards when planting the train, the front pallet arbour hole at the top is an eccentric bush, so if the planted centre ends up being a bit 'off' it wont matter or be obvious,
If not already done, I'd also leave cutting out the centre frame panels until you've marked out the pivots centres, that way you can scribe the plates for exposing the 'straps' either side of the pivot holes equally to ensure that the holes are actually central, it'll help keep things tidy.
if you're building this clock from Wilding's book and you don't have a depthing tool, you'll probably find an irritating reference on page 45 to the Wilding depthing tool being in his first series, unfortunately he doesn't state the 1st series of what, I have his 1990 book and the earlier 1979 hardback of this clock and it states exactly the same in both,
The drawings and details of his depthing tool takes up about a page and is included in the Crystal wheel Skeleton clock and also his 'Tools for the Clockmaker' publication, so it's a bit mean IMHO to have left it out of this book,
If you don't have a depthing tool and would like details of Wilding's fairly simple tool for the job, let me know and I'll scan the details for you,
I'm about half way into the same clock BTW.
John.