Okay, so I started my first build a little over a year ago.  It was a solid wood Tabak cigar box.  I thought, "For my first one I will go all out so that subsequent builds will just be a sinch!".  I went for a fretted, 4-stringer. 

I used red oak for the neck, no finger board originally.  I used some old Gibson tuners I had lying around, and wired a Fender neck pickup in series with a piezo disk (placed under the bridge position). Things were going great.  I cut out star sound holes to match the stars in the logo on the box.  It looked sharp.  But once I strung her up I soon realized the frets were off and she wouldn't intonate for anything.  I learned I didn't measure correctly from the middle of the nut bolt.

Now, so you know, instead of giving up I built 2 fretless (which turned out great and sold quickly) and a dulcimer scale, fretted Cookie-tin-jo (which took some additional work but now intonates and plays great).  So, now to my question (and back to my first failed build)... 

I decided to fix this I would remove the frets (which by the way are pieces of coat hanger I slotted the neck for and glued into place). After filling in the slots and fret markers I added an 8th inch fingerboard on top of the existing neck.  I then cut slots and glued the old bits of wire back down, but this time I added a zero fret and marked off my 25" scale measuring from the zero fret.

My harmonics work fine (as they did previously), but the actual fret intonation is still off. Could this be because of the huge bolt I am using for a string guide?  Can the strings actually rest on the zero fret, and should they?  Should I slot the bolt (string guide)?  The action is set to about a 16th to three 32nds of an inch at the first fret, and about two to three 16ths of an inch at the 12th fret (will provide pics if need be when I can).  By the way, the zero fret is a slightly larger diameter (gauge) wire than the other frets (think of it as 12 gauge vs. 14).

I am more sad and disappointed than frustrated (although extremely frustrated).  Any help would be greatly appreciated. 

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http://www.stewmac.com/FretCalculator give it a try works for me Barkingwood Cigar Box guitar

That's actually what I used, in combination with a 25" scale Washburn electric guitar I have.  I measured the frets out and then compared to the Washburn neck. 

Nut to Bridge, skip other guitar

Your solution may be easier than you think. If your frets are distanced from each other properly (the easy way is to make a fret template from an existing guitar), the distance from your 12th fret to the bridge should be twice the distance from the nut to the 12th fret. In other words, the 12th fret should fall exactly halfway between the nut and the bridge. If it does not, you will never get it in tune! Even then, you sometimes have to "tweak" it a bit by moving the bridge a little forwards or backwards, until you get it to tune harmonically at the 12th fret, to match the open tuning. I've learned not to finalize the location of the bridge until I've got it to tune correctly. Some make a "floating bridge", usually of a bolt or threaded rod or key, something like that, and don't glue it down so that it can be adjusted to tune properly. For me, I like to get it to tune right, then anchor the bridge so it doesn't fall off or "lose it's place" when changing strings. For more information about how to create any scale length using "The Rule of 18", see my page and blog on the subject. Hope this helps you get straightened out! Good luck.

12th fret measurement is 12 and 5/8th inches (an 8th inch off, but something I would think the floating bridge could easily fix).  Other crazy thing is that I broke out my slide, and slide positions above the frets check out correctly (now super frustrated).  I'm about to rip the frets off and just have it be a slide guitar and swear off fretting completely!  I thought doing a zero fret would be my silver bullet... :(

Agreed. If it sounds right with a slide there's nothing wrong with your fret job.

Where is the zero fret in the picture? I can only see a bolt nut.

Can you post a pic of the string height at the nut? If the action is too high it will cause the strings to bend when you fret them and they will go sharp.

Have a look at this video:

I learned early that you have to measure nut to fret for EVERY fret....if you measure fret to fret, unless you are extraordinarily precise, you will be out by a long way by the time you get to fret 22....

Even if you are extraordinarily precise you'd still likely be off too far after stacking all the tiny errors of that many measurements going fret to fret. 

Oh ya, nearly forgot: it's a CBG.....it'll never be ferpect....that's why they are better than Ikea builds......Just add gain and reverb and no one will ever be able to tell..... :-)

no one answered the question "can (and should) the strings rest on the zero fret?".... YES, YES, YES... otherwise your CBG thinks the bolt/string guide is the bridge and all the spacing will be off. Your scale length will be from the Zero fret to the bridge. If it's still intonating badly, then the next suspect is string height.... One of the strengths of zero fret setup is usually nice fast action... ditch the coathanger wire for real frets. Too much work for inconsistant results....

Thanks again Sam, I have some pics to post on my phone, but barely have time to type out this reply (wife is out of town and I got my two kids running around getting into everything).  Thanks for the advise, I wasn't sure about the zero fret, just something to try (just never had or made one).  If I can't get this figured out I am probably going to have to trash the neck and start over.  But before I do anything that brash I will post some pics on here.  

Here are the pictures I promised.  You'll see the bolt used as the string guide, the zero fret, and the action at the 12th fret.

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