Shaft Alignment with Extensive Structure Work

I have a friend who is working on a naval vessel of 58 Meters length & beam 8 meters. Shaft length is 62 Ft overall, there are three intermediate shafts of 13 Ft, 13 Ft & tail shaft is 36 Ft. The dia of the two 13 Ft shafts is 4.7 in & 5 in respectively. Extensive rebuild structural work for re-lifing has been done including renewal of struts or "P" Brackets as they are called locally. Four shafts, two inner & two outer. The problem is is with the two outer shafts which have 3 "P" Brackets each.

Now the problem is that alignment was done using the piano wire. They started from the stern & proceeded inwards. When they reached the starboard gear box coupling they discovered that the wedge with the intermediate was .0056 in at the top & the gear box flange is .079in higher then the intermediate shaft. Similarly, when the same process was done on the port shaft they discovered that the wedge with the gear box coupling & intermediate shaft was 0.0154in at the top & the flange was 0.013in higher then the intermediate shaft. Engine length is 9.2 Ft mounted on rubber clad resilient mount

The question to all those experienced marine experts is:

a. Can they adjust these by shimming of the gear box & similar adjustment of the propulsion engine, which is on resilient mounts.

b. Will these adjustments have any effect on the performance of the engine & the vessel.

c. How much of correction is allowable

An early response will be appreciated. Thanks