Hi,
For what it's worth when I bought my own 350 GTR back in 1986, the previous owner had had both barrels Nikasilled and fitted new OEM pistons and rings. I've run it with no problems ever since, and the barrels have now done around 18,000 miles and still look nice.
The only problem is finding someone to do the re-coating. My barrels were done via Mahler in Germany who did a lot of re-coating for the yamaha racing boys, and the then owner had some "inside" contacts in the racing world.
Another pal over here (England, that is) recently completed a replica of a 1964 Yamaha 250cc twin GP racer (the RD56 if you know the model), using a standard 350 GTR engine in a highly modified GTR frame. He had his barrels re-nikasilled by a local firm, and has subsequently done a lot of "parade" laps at Classic meetings, including laps of the Isle of Man TT circuit and Assen. No problems whatsoever with the barrels, and his motor is run to 9500rpm in 6th on the standard gearing. The expansion chamber exhaust and full fairibng help, but I guess that tells you that re-coated barrels properly done are as good as new ones.