Neck Troubles

This is more of a repair than a build, but I wasn't sure where to put it. (Mods can relocate if a better place is around).

I have a tele clone that I'm fixing up because it was cheap and a good project to revamp. The problem I'm finding with it is that the intonation is terrible and seems to be farther off the farther up the neck you go. Either it's a fret issue or what I believe as more likely, a neck set issue. I think that it is off kilter, because the intonation is worse on the higher strings than the lower. The main question is how I would test this, just use a tuner and find how far off intonation at each fret? (seems like a long process, but I'm up to it if needed).

And also, how do I go about fixing it? If it is improperly set, then how would I fix it? shave and shim? But what would I do about the mounting holes in that case? Any help is greatly appreciated. I have already learned immense amounts from this site, but am just not sure how to proceed with this.

The intonation issues really bug me (I plan on making a fan fret someday because of the intonation, I have rather sensitive hearing to off key things and it bugs me a lot having half of my chords being off) I'm actually at the point where I may just flip the guitar for slightly more than I bought it for (because I've put some work into it since then), it's almost more hassle than it's worth, but it's a challenge and learning experience.

Measure from your nut to the 12th fret, and from your intonation area on the bridge to the 12th fret. They should be the same distance. In other words, the 12th fret is the middle point between your nut and saddles.

You may have to move the bridge, or you may adjust it. You want to have the note be on the same pitch at the nut and at the 12th fret (the E-string will play E both open and at 12th, etc).

Intonation and scale length are a compromise with a conventional style neck, at best.

Bad intonation is always going to be worse the farther up the neck you go. Although neck relief influences intonation it's not likely "neck set" is the problem. The procedure for intonation is discussed in several posts on this forum, so I won't repeat. Try adjusting the saddles. Unless the manufacturer really screwed up and placed the bridge in the wrong spot, the normal intonation procedure of adjusting the saddles so that the open string matches the fretted 12th string should fix your problem. If the 12th fret note is flat, the saddle needs to move forward. If it's sharp, the saddle needs to move back. In some cheapo guitars it's almost impossible to get a perfect intonation on the low E.

And to add with what Bud said, you have to set string action FIRST (neck relief, saddle hight, nut hight etc.) before adjusting intonation. New strings are a good idea as well.

Perhaps a bit less tedious, but potentially telling, is to make sure you've got the right scale and the right neck. First, as OpenGCapo4 mentions, measure the distance from nut to 12th fret, and then from 12th fret to bridge. If it's true to OEM Telecaster, it should be 25.5. Next thing is to make sure you've got a 25.5 scale neck--that is--the frets are in the right place for a 25.5 scale. It is possible to place a neck with the 12th fret in the right place, but other frets will be off.

So after determining that it is a 25.5 scale, look up a 25.5 fret location table, and carefully as you can, measure the fret locations with the most accurate measuring instrument you can get your hands on. If the higher frets are not where they should be, you've either got a sloppy-built cheapo neck, or a neck built for a different scale.

Sorry, I should have mentioned that this is a cheap kit tele made by a non guitarist. I have already adjusted everything, including the intonation and know how to do so. Thank you R. Stratenstin, I will check the scale, as it could easily be that.