Patty
Everyone so far has made sensible suggestions but I guess you want ideally to take one definite course of action and see how it goes.
* I suggest you ignore for the moment the possibility that your maker simply got his fret spacing wrong and try to improve the intonation, not perfect it;
* Given the materials used, you need to replace the bridge (certainly) and nut (possibly, though it's a more delicate operation), and preferably in a hard material like bone or corian;
* The bass D string seems pretty much OK with your current set up, so use that as your marker (don't worry about the intonation of the bass string beyond the 12th or so fret - it's usually pretty unplayable up there anyway);
* The middle string is mainly sharp, which suggests you need that part of the bridge to be further from the nut (you make the bridge using three different facets);
* The melody string(s) - the pair won't/can't really be different - is mainly flat, which suggests the bridge facet needs to be nearer the nut. NB we are talking small differences in distance from the nut of maybe no more than 1mm between each facet.
* So far, so standard with a tuning of DAD and a 12/15/22 - 28 set of strings. But your bridge is floating I think you said - it doesn't have a fixed slot? This means you can fine tune the position of the bridge - and SLANT it slightly if necessary - to get the intonation across and up the fingerboard acceptable, if not perfect.
...It will of course be easier if you ask a luthier to do all this for you, but it's perfectly possible to do it yourself with a little care.
Good luck!
Geoff