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Intonation Problems Building 5 String Fretless

OK, I'm fairly new to the forum, posting at least, but here goes...
Sorry in advance for the length, i just want to be as detailed as possible in explaining my problem and how i got there...

I'm building a 5 string fretless bass. I've built several guitars before but this is my first bass project. I bought a Cort Action 5 Bass body. The neck was a project alone. I bought an Eden 4 string FRETTED neck and drilled a 5th hole so its ultimately a 4+1 type neck, 4 on top 1 on bottom. I pulled out the frets, filled in with wood filler, and put many coats of polyurethane on it. I was scared the neck would be too thin for 5 strings but it actually looks great and the strings fit perfect. I put the bridge on, drilled the holes through the body for the strings and just to test the neck to see if it sounded OK after pulling the frets out i strung up 2 strings (still gotta but a set of flatwound 5 strings). The neck sounded great, no dead spots and no valleys or hills in the fretboard. I need to sand down the nut though because its high for a fretless.
But here is where the problem begins. I hit an open note, and then i go up to the octave, or where it should be, and its a little high, the octave is actually about where the 11th fret would be located if there were frets. I have messed with the bridge as much as i can, but it doesnt make much difference.
Has anyone ever had this problem before? Does anyone have any suggestions or ideas on what i can do to fix this problem? I'll post pictures so you can see the style bridge im using and so you can see what it looks like. im stumped and dont know what to do.

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so you mounted a 21 fret neck where a 24 fret neck once was? hmmmmm this might be the place to start thinking.
Then to the scale length. 34" scale length, measure from front of nut to bridge saddle, if it's like 33 1/8, you might need to move the neck back about an inch.

BTW...assembly of pre made parts is just that, assembly.
 
ok i just measured it, 32 inches total, 16 inches to the octave, which is located exactly here the 11th fret would be located. 12th fret is at 17 inches, making the total length to the bridge 34 inches, but 34 inches is almost hanging off the bridge body, about 3/4" to 1 inch from the end of the body.

Any ideas? thanks for the lightning quick reply also :)
 
From the saddle to the nut should be 34". When you bought the new neck, you porbably got one that is slightly shorter in length (as far as frets) or doesn't sit in the pocket the same. Therefore you have to move the bridge so that when the saddles are halfway in their slots, the saddles are EXACTLY 34" from the nut. Then make you adjustments... fill any holes if you need to.
 
From the saddle to the nut should be 34". When you bought the new neck, you porbably got one that is slightly shorter in length (as far as frets) or doesn't sit in the pocket the same. Therefore you have to move the bridge so that when the saddles are [del]halfway [/del] zeroed in their slots, the saddles are EXACTLY 34" from the nut. Then make you adjustments... fill any holes if you need to.
Fixed - no need to centre the bridges on the witness point, you can zero the saddles and then put them on the 34" witness line (minus a little bit for changing tunings/gauges down the road)...
 
im looking at moving the meck up a little bit now Stumbo. i only have enough room on the body to move the bridge back 1/2". that means i'd have to move the neck up 1 1/2" to get the full 2 inches i need. It'll be rough on screwing the neck to the body with it moved up that far, and the gap thats between the neck and body would look hideous... But... its still an option. im thinking of just buying a 24 fret neck, but finding cheap bass necks online is hard. i love how the neck looks after i filled in the frets so i hate to even think about it, but im almost thinking about painting the fretboard so you cant see the false fret lines. thats the worst case scenario tho and i'd hate to have to do that...
 
Fixed - no need to centre the bridges on the witness point, you can zero the saddles and then put them on the 34" witness line (minus a little bit for changing tunings/gauges down the road)...

I'll have to post pics of my saddles later to show you why... my saddles are drastically varied on my Ibby K5. They and a slight "S" shape to them. If I placed a bridge on a newly built bass such that the saddles are in the middle of their travel area when I measure for 34", then I have 1/2" on space to move the saddles. When strings wear out, they tend to vibrate at different frequencies; therefore the require various amounts of length as they age in order to acquire perfect intonation. Considering I play on old strings a lot, it's best to have that 1/2" of play either way considered each string wears a different way than the others. I know this from experience... I've needed more than 1/2" when my 3 year old strings wore out, no joke.
 
In theory VinKreepo, you're right, however when one intonates from zero, the string is always lengthened, not shortened, unless you're putting on lighter string gauges (for example a piccolo bass setup). As strings age, they stretch, causing the need to move further from the scale line, not closer to it. What will happen by centreing the saddles before mounting the bridge, is if you choose to detune, or use higher gauge, you'll run out of room, or at least end up moving the saddles so far back that the breakover angle begins to get too steep. There isn't a need to put the saddles in the centre of the bridge. You can move them back from zero by 1/8" and have plenty of adjustability...
 
In theory VinKreepo, you're right, however when one intonates from zero, the string is always lengthened, not shortened, unless you're putting on lighter string gauges (for example a piccolo bass setup). As strings age, they stretch, causing the need to move further from the scale line, not closer to it. What will happen by centreing the saddles before mounting the bridge, is if you choose to detune, or use higher gauge, you'll run out of room, or at least end up moving the saddles so far back that the breakover angle begins to get too steep. There isn't a need to put the saddles in the centre of the bridge. You can move them back from zero by 1/8" and have plenty of adjustability...

I guess that's my problem... I try way too may different strings/tunings haha
 
You could make a wooden floating bridge and the either run the strings through the body or make a tailpiece.

My recommendation? Keep it at 32" scale, cover the fingerboard with black epoxy to cover up the old (now misplaced) fret slots, and use some contrasting dot side markers to indicate your position. That's what I would probably do.

Of course, it's your bass... That's just my $0.05 (two cents adjusted for inflation). :)