Shaft alignment with fixed mounts

I am planning on aligning the engine in the Mustang next weekend and am looking for tips for this type of mounting system.

I don't believe this engine was ever re aligned after it left the factory. The engine sits on wedges that are on wood mounts that sit on the stringers. It appears that when the engine was installed at the factory, they lined it up and then drilled holes down through the mounts into the stringers and lagged bolted it up.

After re setting the engine, the angle appears correct, but the whole engine appears to be up about 1/4". I figure I can take the lag bolts out 2 at a time and knock the wedges forward until the engine comes down. As the engine will be in the same place, I can then re drill the holes through the wedges and they should line up with the existing holes in the stringers. Does this sound right?

Also, I am wondering how much the shaft can be moved into position. There's a new cutlass bearing, but it appears that the weight of the shaft does weigh the stuffing box down a bit and it may want to come up just a little. Any ideas? It seems like this is more art than science.

Hopefully, we got this lined up yesterday. There's 2 parts to the alignment: having the planes of the flanges parallal and having the axis both up & down line up. Initially, it all looked good, except the engine was 1/4 inch high. The shaft was centered in the log and the flange really didn't seem to be putting much, if any downward pressure on it. We tapped the rear wedges forward about 1/3 of an inch and the flanges actually came into a very good plane with each other, except horizontally, they were about 1/8" off. Engines with fixed mounts cannot be moved side to side without relocating the whole engine either a 1/2" forward or backward. I put a board up against the side of the shaft and moved it over the 1/8 and surprisingly, the alingment seemed very good with the feeler guage. We bolted it up and it turns freely and seems fine. There's got to be some give with the axis alignment, hopefully we're within those tolerances.

I would say that the best way to re align a fixed mount engine is by drilling new holes in the stringers from scratch, but that didn't fit our application. If we were doing it again, we would fill the old holes in the stringers with epoxy and place the wood mounts on the stringer 1/2" forward of their old location, keeping them loose until the engine was in alignment, then drill & lag bolt everything in.