It's a 04 MIA Stratocaster, 4 bolt tilt neck, and the 2 point floating bridge. I'm using 9's, and the intonation is spot on.
I've always been able to set up my own guitars, but this one has me a bit flustered.
The action is great from the nut to about the 10th fret, then it starts getting a bit higher off the neck. The G string has a small bit of frettin out rattle, even in the first few frets, but nowhere else. Right now I have 3 springs in the trem cavity.
Do I tilt the neck up towards the srtrings a bit more, then raise the individual strings? Advise please !

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Life is like a sh*t sandwich. The more bread you have, the less sh*t you have to eat.

This is just me, if the rest of the action is good, I would just adjust that one saddle up a little bit until it is where you like and gets the fret out taken care of. I wouldn't go for any neck adjustment because you might get more issues.
Hope that this helps.
ABS

You might need to have the frets leveled & crowned. I had a simialr issue on my Telecaster even before it had a great deal of playing time. I took mine to a luthier who performed the work and it cured the problem. Well worth the $85.00 fee.

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"My mind is a raging torrent, flooded with rivulets of thought cascading into a waterfall of creative alternatives." Blazing Saddles...

First make sure all the strings are clearing the first few frets when played open. This is controlled by nut slot height and the condition of your frets.

To do a simple bounce test. Hold each string down (or capo) on the third fret in the middle. Bounce the strings directly over the first fret. They should not be resting on the first fret wire otherwise the slot is too low.

Shimming or micro tilting the neck is normally not required.
If your unable to get enough saddle range to set the action then you do need to adjust it.

What I would do in this case (and consider this before you do it to make sure its not beyond you skill level) is set the neck as straight as you can get it.

Use a straight edge (or improvise with a long steel rule) and check the levels of the frets tops. You will be able to see if you have high or low spots.
Set your saddle height and don't worry about intonation just yet.

If you are getting buzzing on the lower register (frets near headstock) only then you can use the truss rod to add more relief to clear them.
If its in the upper register (near the bridge) then you should raise the height slightly.

But remember you will get buzzing no matter what if you try a low action. You can normally feel your way through it though when the neck is straight. Always setup with new stretched in strings.

If you can get a decent action while playing open and playing down the strings on every fret then set the intonation and tweak height adjustment again if you need to and your done.

Obviously if your frets are all over the place then you need to have it fret dressed with a luthier or good setup tech.

It doesn't have to be high frets.
It could be but it doesn't have to be.
It could very well be a slightly misaligned neck.
The beauty of the MIA Strats is micro tilt.
Micro tilt can solve a miriad of issues.
Just remember that with micro tilt a little goes a LONG way.
Make very small adjustments and only test your action after tuning to pitch.
First, set your relief using a capo and a feeler guage.
Be accurate and do it right.
ALWAYS double check your state of tune before checking relief.
In fact double check your state of tune before checking any aspect of setup after a tweak..
Without proper tuning the test is meaningless..
Don't worry about action at this point, just get the relief right.
Then adjust the angle of your neck so the action is reasonably uniform.
Then saddle height and last saddle position.
Of couse absolute last would be pup height.
There's a small chance you may have to tweak your intonation after using micro tilt.
If you can't dial out the problem this way then you should look at fret height.
Hacking up the fretwork should be a last resort.
It means something went seriously wrong in production.
That's not very common on modern MIA guitars.

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Just think of how awesome a guitar player you could have been by now if you had only spent the last 10 years practicing instead of obsessing over pickups and roasted maple necks.

What are those?

+1!

Arjay

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"Here's why reliability is job one: A great sounding amp that breaks down goes from being a favorite piece of gear to a useless piece of crap in less time than it takes to read this sentence." -- BRUCE ZINKY

if your checking the straightness of the neck on the frets your not getting a clear reading of the actual neck. stewart macdonald sells a neck level thats notched to check the neck. i have one . it tells a whole other story. you level the neck with that then ckeck the frets with a streight edge. youll see if you need fret work instantly. i was surprised how far off the necks on my guitars were. but using this method i got everything back where it belongs.