First off, half gaskets are an age old accepted means of final alignment. With machine tolerances improving over the decades, they have fallen out of general use, but they used to be done quite frequently. With the ammount of misalignment you mentioned, I wouldn't be surprised if your piston was touching the liner at the top or bottom of the stroke. This side loading is what is causing the excessive side bearing wear on the big end.
What is probably happening is that the side holes where the TRB carriers set are not even with the deck. This makes the crankshaft not perpendicular with the bore and results in the piston-bore misalignment. probably the easiest way to determine what is what is by using a precision machinists bubble level. I used a 6" model made by Starrett that pointed me right at the issue. But if you don't have access to one, they are a little spendy. Another way can be done with a $7 1" dial indicator from Harbor Freight and some scrap metal and a large straight edge. Both methods involve removing the cylinder/piston from the block. With the level, you shim the block in it's mounts till the edge of a bubble is against one of the indicator marks on the bubble vial with the level setting on top of the block(deck). Then you set the level down on the crank and compare the readings. You need to do this at several points of crank rotation, and is best done with the flywheels removed. Ideally, the crank should be level with the deck. This type bubble is also precise enough to tell you if the crank is bent as the readings will change as the crank to rotated if the crank isn't true.
The dial indicator method is similar in that you use these tools to compare crank to deck. Place the straight edge across the deck, and using a piece of scrap clamped to the attach point on the dial indicator to put the top of the crankshaft within the 1" range of the dial indicator when measuring straight down from the straight edge placed across the deck. Again, this is easier if the flywheels are removed. It dosn't even require a perfectly straight edge, if you turn the whole rig around to measure the other side using the same points on the straight edge. Again, proper alignment should yield you the same measurement from the bottom of the straight edge held across the deck, to the top of the crank. You can also use this method to tell how true the crank is by comparing readings taken as the crank is rotated. If you get a difference from left to right, then the deck is not aligned with the crank. If you do not note any mis-alignment in the crank to deck measurements, then the problem lies in the piston/rod, or the cylinder-liner relationships.
You can also pull the crank out and measure this same way as you did the crank using the dial indicator, from the deck straight edge to the bottom of the TRB holes in the side of the case. This will show differences in the TRB carriers if any. This is where my misalignment on my block was. The hole in the block on the non-starting side was about .015" lower than the starting side measured up to the deck. How I fixed mine was to take the TRB carrier on the low side and chuck it in a lathe. I then offset it in the lathe and took about .015' off the top half of it's circumference, of the portion that fits into the hole in the case. This allowed that TRB carrier to be slid up as much as .015" when in the hole. I re-assembled the engine and on the bottom edge of the case hole, I inserted old feeler gauge blades and gradually shimmed up that side untill my differential squish was equal on both sides. I wound up with a .013" feeler gauge shim under the TRB housing to achieve equal squish. I tack welded this shim in place.
Why did I do this, well because my engine had never been run, I had the time and tools available, and most days I am a nit picky SOB... In the measuring process, I also noticed some tooth mis-alignment/uneven wear when I checked the idler gear mesh, and this adjustment helped center/even out the measured wear patern. My short block was delivered with a half gasket under the starter side of he cylinder that yielded less than a .001 difference in squish across the piston, and I am sure that it would have happilly ran that way also... The decision is up to you as to which approach suits your needs and wants the best.
Good luck.
