Kevin,
If the new holes won't overlap the old ones, I would go with Dan's wood filled approach--with a couple of exceptions.
First, don't force the dowels into the old holes. That builds a latent splitting force into the mount and doesn't give you anything in return. Epoxy is dense and pretty incompressible, and will carry any compressive loads you are going to see in the repaired mount. So you don't have to aim for wood on wood. In aerospace applications you always want a minimum bondline thickness to ensure continuous adhesion. For most epoxies the recommended bond line is somewhere between .006 and .012" thick. It is necessary on non-porous materials. The fact that wood is porous gives us some leeway in the motor mounts repair business. The porosity is further enhanced because much of the hole is actually end-grain. Still, I would rather have some clearance and get a full bond. Obviously, get all the oil out that you can on the old holes. Epoxy isn't going to stick to an oily surface--although it will mechanically "lock in" to rough surfaces--so what you really end up doing is "packing the hole," not gluing in a plug that will transfer load across it like the hole was never there.
Next, I would use maple or birch for the plug. You want to match the hardness and try to carry load across the hole.
If the mounts were beefy and the engine is not a beast, then having old holes is not such a big issue. Having old holes where oil can continue to invade the wood and soften it up is a big issue--over time. If you are not worried about the mount strength, you can fill them up with JB Weld. It is a metal-filled material with much better epoxy than I would have expected. I did pull test coupons on it for fun along side a number of other aerospace grade structural epoxies. It won't match an unfilled structural grade epoxy, but it quite good.
I added a picture of a motor mount "refurbishment" I did on a friends Legacy. It has a monster 4-Stonker in it and the whole front end was soft. So everything forward of the wing got the full treatment. The engine mount holes were way oversize and not particularly straight. The engine would shift around in the cowl and cause trim and other problems. I cleaned, then filled the holes with JB weld. Then, using a steel drill guide clamped it on and redrilled. It came out fine.
Probably all stuff you already knew, so I apologize for maybe restating the obvious....
Dave