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Alright, so I don't have a lot of experience with guitar repairs, so I got this Mexican twelve-string guitar on Craigslist with a busted bridge.
So, I found a replacement, after quite a bit of searching, but it was a bit rough so I've been working on it before I put it on.
The only thing that concerns me is that the saddle slot sits about three eights of an inch higher than the old one. I'm pretty sure that's too high, so I wanted to know what the best way to fix that would be.

Hi Rick and welcome to the OLF.

Replacement bridges for acoustics are often made as needed by Luthiers who are doing the repair. Even though in the case of Martin replacement bridges are available they typically are not exact replacements in one way or another so we just make them as we need them.

For more obscure guitar brands replacement bridges are often impossible to source so again we make them and in making them our selves we also have the opportunity to correct things such as saddle placement if the original was in the wrong position.

3/8" is WAY off in terms of forward or aft positioning. Think of it this way the "speaking length" of the strings (between the nut face and the break spot on the saddle) determines the intonation and the intonation determines if the thing plays in tune up and down the neck. If the break spot on the saddle is .007" off this will result in a one cent difference in the intonation or how well the thing plays in tune. 3/8th" is .375" or slightly more than 53 cents off..... not good.

So after all of this if it makes any sense to you my recomendation is to simply make a new bridge or have a Luthier make you one if you don't want to do it. You or they can determine the exact spot that the saddle needs to be, optimize the existing bridge foot print, likely carft a better looking bridge too and it's likely that you will improve the instrument over what it ever was even when new.

Also I am not completely sure that you are speaking of the forward or aft positioning of the saddle slot or the depth of the slot. 3/8" higher in saddle slot depth would be no slot at all.... so I am assuming that you mean slot placement and not depth. Don't want to make an arse out of you or I my friend if I am misunderstanding you.

Hope this helps.

Hey, thanks!

Yeah, I don't think I was very clear, sorry.
I did actually mean the depth of the slot.
The original one was a thin piece of wood, and the slot was cut down to where the saddle would hardly be raised above the body.
The new one I picked up was a much thicker piece of wood, so the saddle would sit 3/8 of an inch higher. I feel like that'd have a major affect on the action, and I'd assume on the tone, especially higher on the fretboard.

3/8" sounds really high. You could put the old one on and use a caliper to measure the total height to the top of the saddle. Then work backward from that to check to see if you can get the new bridge and saddle worked down to that height. You can pick up a compensated bone saddle pretty cheap. See if you could sand down the saddle to fit the slot and come up with the height of the old set up.

Deepening the slot in the bridge will be a bit more of a challenge. You want the bottom of the slot to be flat so the saddle makes good contact with it and the sides of the slot. I have done slotting by chucking an end mill in the drill press. Then set up a jig so you can slide the bridge across the bit. Note this can be not only dangerous to your fingers, but any miscalculation can ruin the bridge. BTW, if the saddle isn't tight, I've layered up super glue on the saddle and then flattened it so you can almost pick up the guitar by the saddle. That's the mark of a nice fit for the saddle.

See how much wood there is between the bottom of the slot and the bottom of the bridge. You might be able to sand the bottom of the bridge a bit and sand the saddle to hit the mark.

Good luck.