For example if I have a Clockwork Spy can I upgrade it into a Clockwork Servant or from that to a Clockwork Golem?
There is no given process in the rules for doing so. You'd have to convince your GM it was a good idea to allow it.
I'd allow it under the same principle as upgrading a magic item, paying the difference in cost between the two creations.
The spell Transmute Golem exists, but it's generally better to just make a new one.
It's also only for Golems. So it's up to your GM if that means that non-Golem to non-Golem would be worth a 7th or 8th level spell or if it'd just require a separate 9th level spell researched if they're inclined to allow that sorta thing.
As for by crafting, nothing dealing with that in any rules I've laid eyes on. So that's another thing you'd have to use your powers of persuasion and social engineering and apply them to your GM to determine what is or is not possible.
Of course, they are due for a publication all about construct creation here in the not-so distant future, but I wouldn't hold out on that addressing your area of interest.
Well okay the big thing I'm looking for something to do with Wyrwood. As a race they are middle of the road in the way of base power level. As constructs they suck on toast with no nat armor or anything apart from the base construct block and even then they lose out on some of it. So I was just wondering if there was a way to upgrade them to a different construct rather than have to break them down into CR's so I can apply craft construct modifications to them. They are akin to wood golems in a sense (if you look at their description) so I was thinking about starting there and moving my way up as money and CL allowed. Thanks to the latter CL restriction doing this really would not be that powerful per level.
And for the record that is probably the most useless waste of a ninth level slot I have ever seen. You could have wish, or an expensive waste of time.
Not by the rules. You would have to get your GM to make an exception.