This is a pretty good read on the topic of rod to stroke ratios. Even if you don't understand all of it, I think you will get the main points by reading it over once.
Piston Motion: The Obvious and not-so-Obvious, by EPI, Inc.
Figure 9 is especially telling - this graph shows a piston's velocity, acceleration, and travel when it is connected to a rod and stroke that develops a 1.54:1 R/S ratio in comparison to a 2.56:1 R/S ratio. The difference is very little even though the R/S ratios are very much different.
If you use a 5.965" rod and a 3.625" stroke, your R/S ratio is 1.65. Say you go with the 6.350" rod and the same 3.625" stroke, your R/S ratio is 1.75. Remember the
figure 9 graph - this was a comparison between R/S ratios on extreme ends of the spectrum. The differences in piston velocity, acceleration, and travel were small (of all the characteristics, 5% was the minimum and 10% was the most). The difference in maximum side loading is 2% according the
Figure 10. Still not all that much. Think of how small the differences would be in piston velocity, acceleration, travel, and side loading if the figure 9 graph compared a 1.65 and 1.75 R/S ratio.
I am open to any corrections or additions.