.250
I've got a 99A from the 70's that is a good shooter with either 87 or 100 grain Winchester loads. I've also had excellent results with 100 grain Noslers loaded over either IMR 3031 or Reloader 15.
What condition are your reloading dies in? Sometimes a die will seat the bullet with considerable run out causing painfully assembled reloads to scatter when factory rounds shoot well. A drastic velocity change can also effect the grouping with a two piece stock. The fitting of the forestock is always worth a look when trying for better accuracy from a 99.
I think that 1.25" groups however are quite fine for any deer/coyote hunting I require from a .250 using good bullets.
I bought my .250 back in 1996 when living in the north as the local store had tons of Winchester and Western .250 ammunition (87 and 100 grain). No one in the community had a .250 anymore so I bought many many boxes for $2.50 a box and still have some. I tried the little "pest" gun and to my considerable surprise it worked wonderfully. I was very conservative about my shots until I learned that even the 87 grain bullets would fully penetrate a mature caribou. I used it to take a crazy number of caribou, four black bears, one wolf, and a few seals. Great little round in a 99.
Regards.