I am interested in luthier work and decided that before I make a guitar, I should try to make my own guitars better.

With that in mind, I have some questions about the nut and saddle, and what your guitars look like.

I switched from whatever was on my acoustics to custom lights 0.011 to 0.052.  I recently learned about neck relief and adjusted my tuning rod.  This was after lightly sanding the saddles down to help lower the action. (Cart before the horse, but I'm learning).  The guitars both have some harsh frets, which may be due to worn strings and high frets.  They are also both slightly sharp when fretted.  (My ukuleles are too, so I am not sure if there is something I am universally doing wrong with tuning/setup, or if it's just the same problem among all of the acoustics).

Until recently, my solution was to tune all the open strings down about 10 to 15 cents so that my fretted notes would be in tune.  This works well for playing chords.  Now that I am learning about scale length, I see that both my guitars are slightly off on scale length.  This makes me want to do two things: replace the saddle and replace the nut.  I am thinking about trying to cut my own bone nut and find a compensated saddle.  Before I do any of this though, I thought I would post pictures of both nuts and get opinions from the crowd.  What do your guitars look like?  Any other opinions out there for fixing acoustic intonation?

How do you know they are off on scale length. Are you measuring from the nut to the twelfth octave fret and double the measurement.

Yes.  They are not off by a lot, but they are not the same.

What is the scale length given by the maker compared to the measurement. That looks like an Alvarez head stock. I have always been impressed with them 
for the price range.

When I was building guitars I would buy cow bone from the butcher, boil it at home, cut it into blocks, bleach it then cut it to desired size.  I also used Corian from time to time and used to sell boat loads of it on ebay.  I say go for it, as long as you have the tools there is nothing magical about any of this stuff.

I haven't found the manufacturer's specs. It is an Alvarez MSD1 and it's fun to play.  The nut to 12th fret is 11 5/16, and 12th fret to saddle is barely longer at 11 3/8.

I took the strings off last night and oiled the frets and bridge. While I was looking at it, I noticed that the saddle was leaning way over under string pressure.  I looked at the bottom and sure enough, I hadn't been careful enough when I sanded it previously. There was a slight tilt. So I sanded it square, lightly took out the gouges where the strings have dug in, and cut a piece of paper to help fill in the gap.

It's standing up a little straighter now, and most of the strings are closer in tune.

Something is different in the tone now, and I am guessing it has to do with the paper I used to fill the gap at the side of the saddle. I'm going to see about shopping for a new saddle.  It could be the oil, or the new strings as well.

I just replaced the nut and saddles on both my electric and acoustic guitar.  I used TUSQ for both. For the nuts (TUSQ XL), I measured the string spacing on my original, and found that I could use one of their pre-notched versions for both the electric and acoustic.

Removing material from the base of a nut or saddle is tricky, as you have discovered.  It can be difficult to keep it square across the bottom.  When replacing the saddle for my acoustic, I didn't remove any material from the base of the saddle.  It came perfectly square, and I didn't want to risk screwing that up. So, I used the original saddle as a guide (I measured the radius of the original saddle to make sure it correctly matched the neck radius)  to draw a proper radius on the new TUSQ saddle.  I then filed/sanded it down from the top, to the proper height (actually, a little lower than the original).  I finished it off by sanding it up to 12000 grit, and then hitting it with some polishing compound.  

For the nut, I did carefully remove some material from the base of the TUSQ nut (because it was so tall), but I did it by putting self sticking sand paper on the steel base of my jointer, and using the guide fence to insure it remained square.  Then, I finished adjusting the string height by using the proper nut files to fine tune the depth of the notches.  Attacking the nut from the top allows you to individually adjust the height of each string, so you can get the radius correct.

I honestly believe the tone and sustain of the acoustic guitar improved somewhat by using the TUSQ material, and, I swear it stays in tune better.  

StewMac carries a variety of nuts and saddles, including pre-notched bone.

Good luck, and have fun with it!

Thanks! These are the kinds of experiences I was hoping to hear when I started this thread.

Quick update on my Alvarez. It sat overnight for the strings to stretch and settle, and give the oil time to set. Tuned it up and have near perfect intonation all along the frets. There's a little buzzing here and there, which I think is from my fingers lightly touching adjacent strings.

Now that I have it set up better, I can tell I lowered the action a little too much. That's probably why the slightest touch causes buzz.

I have been looking on Stewmac for tools and materials, and watching videos about luthier work. A lot of people describe the differences between bone, bleached bone, TUSQ, and metal; but no one plays the difference so I can hear it.

I think I want to try bone for ease of shaping, but I'm leaning towards TUSQ because of the reviews and widespread use (and the softer/warmer tone it is supposed to have).