I have an 1896 Krag that has a Lyman front sight.  I removed the Lyman sight and found that the sight dovetail had been filled in.  I bought a 1903 sight from Numrich that has a slot for a spline. 

I'm guessing that the spline fits into a slot (dovetail) in the barrel, right?  I read where another poster used a set screw to secure the 1903 sight on his Krag.  Other than cutting a slot for the spline, are there any other ways to secure the sight base?

That would be my first choice, a Krag sight, but the dovetail fill is hard.  The 1903 sight slips right on, but I don't want to cut a slot for the spline.  Cutting the old dovetail out or cutting a new one for the 1903 sight is beyond my skill level.

Battis, I used a 1903A3 sight on my Krag.  I used a short set screw to hold it firmly in place.  Did you get a 1903A3 front sight or a 1903 front sight base?
The 1903 front sight base has a horizontal hole through it.  If that base is put on the rifle and you carefully run a drill through that hole, it will cut a groove across the top of the barrel so a pin can be used to hold the base in place.
The 1903A3's horizontal hole intersects the key that would go into a slot milled in the barrel, as you suspected.  I didn't want to try to cut a slot for that key.  That's why I used a set screw instead.  I guess I could've soldered the sight in place but didn't trust my soldering skill.

One of my cutdown rifles has that sight, whoever put it on just drilled a hole up from the bottom and threaded it for a set screw.

I just called Numrich and told them that the pin is too large for the hole in the rear of the sight.  They checked their stock and told me that I'm right - the pins they have listed don't fit the sight hole.  But they're not sure if the pin is too large or the hole is too small, and they want me to send both back.  I said I'll keep the sight and install it another way (set screw, epoxy, bubblegum, etc).

Is the bottom of the sight base thick enough to thread a hole for a set screw?  Machinist I am not.

On my front sight I drilled and tapped a hole in the underside of the barrel because the front sight base band material is too thin.  There's a match-drilled hole in the band that is a close fit on the set screw.  So, basically, the set screw is a post attached to the barrel that the band is impaled on.
I was very careful to not drill too deep into the barrel.  Didn't want a "ported" Krag.

Battis, it occured to me that you could drill down through the top of your front sight base, right in the middle of the dove-tail.  Thread that hole for a set screw.  Plenty of depth for threads there.  Then match-drill a shallow hole in the top of the barrel that the set screw can engage when it's tightened.  After the base is in place, then install the rest of the front sight into the base.  That's what I tried to do first with my 1903A3 front sight but ended up breaking my tap due to being overly eager.

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I measured one of my sporters.  From the butt to the center of the rear trigger guard screw is 12.125", the distance "A" in the pic.  That's a regular military butt plate on there.

I understand what you mean about drilling.  I have a drill press and all kinds of clever ways to clamp things where I want, perfectly square, etc.  Otherwise I'd never try some of the stuff I've done.  I really wish someone would give me a milling machine.