Well, as always, your results may vary, however, I work on two bikes that are both 1397's with stock rods
One has +5" arm with 200lb suited rider and 40 shot. Best et is ~8.90 Best mph is 160. ~1.51-1.53 60'
One has +10" with 255 suited rider and 15 shot with more agressive carpenter cams. Best ET is ~8.80 Best Mph is ~154. 1.40-1.45 60'
Both bikes have a stock output shaft.
Also work on a stock bore, stock piston turbo bike with Carillo A beam Rods and spacer. Best et is 8.30, Best Mph is 174with the stock bore. 1.36-1.38 60'. Also has a stock outputshaft, but I would NOT reccommend a stock output shaft at this level.
Make your own conclustions, but at your power level, I wouldn't do anything other than tune it. You COULD raise your fuel pressure if you se any issues, but you should be fine as is with stock rods (no need to replace them), output shaft, and fuel system. Take a look at your power commander and provided you have the bike tuned would bet you have something in the 18-20 range as your highest numbers. You should be ok up to about 25 in the PC (assuming a PC3, 3R, or USB).
Replace the shift shafts and forks and ge the trans cut, but I'd leave the rest as is, including keeping the same stock rods in that you already have,
John