Might I suggest trying a split-point drill. Solid carbide if you can afford it, otherwise at least a cobalt steel one.
Try going a bit undersized, and then following up with a chucking reamer for your 1/4" size. I think that you can do it from a single side.
If possible, add a bushing to support the drill bit right where it enters the hinge part. That, plus the lack of a chisel point, will likely reduce the wandering of the hole.
To keep the other two holes in line, another bushing between the two ears, hardened steel after drilling to just under 1/4" and reaming to size. Maybe case-harden the bushing, with the Kasenit packed into the hole during the heat cycle.
For holding it -- I might consider clamping it to a angle plate on a faceplate in a lathe, so the hole rotates instead of the bit. (This tends to minimize the wandering a little, too.)
Normally, I would suggest a screw-machine length bit, instead of a jobber's length bit, but I think that you may need an over-length bit to get the full reach.
O.K. Flute length on a 1/4" split point drill that I have in my index (1/4", 3/8" and 1/2" are split point, along with a few tap drill sizes -- the rest are the standard chisel point. If you short-chuck it for the last bit of the hole, and back it out frequently to clear chips, I think that you could manage it. Keep it fully chucked until just before the chuck touches, then loosen the chuck, extend the bit enough and re-tighten the chuck to drill on through. I know that you can get
6" long and 12" long aircraft drills, but wandering would be more of a problem with them, so if you can keep it to a single jobber's length split point cobalt steel bit I think that you can do it. (Hmm ... perhaps an adaptor a bit larger in diameter, and a flat for a setscrew ground on the side of the shank and you could do it with a single chucking.Oh -- you are talking about the two holes, not the single longer hole. A jig with a bushing above the first boss, and a 2" long bushing between them -- all as one piece to keep the bushing holes aligned. Case harden as above.
Have you ever used a split point drill bit? A lot better at avoiding wandering when starting, and likely so also down in the hole.
You have my thoughts above.
Good Luck, DoN.