In between games, I shuffle like this:
Five riffle shuffles.
One pile shuffle (seven piles)
Five riffle shuffles.
IN between rounds, I do an additional 2 pile shuffle. Note that if you make an odd amount of piles, you will never end up with cards in the same place. It's irrelevant if you do this with 60 or 61 cards (statistically, even, it becomes harder to randomise a given amount of cards as it becomes larger, so it'd even be harder to do it with 61 than with 60. This difference is quite marginal, however

As for sideboarding, I used:
4x Phyrexian Negator
3x Coffin Purge
2x Blue Elemental Blast
3x Seal of Cleansing
1x Island
2x Abeyance
1x Balance
Please note that this was a little while ago already.
- The Negators came in against control (as an additional win condition combo with Riruals, NOT as a replacement for the original combo)
- The Purges were mirror hate and possibly for Dragon as well.
- The Seals are insane Dragon hate (and perform well vs. Chalice, too if you fear those).
- The Island is for decks that run either maindeck Blood Moon or are expected to side them in against you
- The Blue Blasts are obv. meant to take out any Blood Moons and fucntion as random countermeasures vs. Sligh as well.
- Abeyance was there for the mirror match and various Long-type combo decks.
- Balance is for random Aggro.
I havent played RTrix in today's meta but it still seems to stand it's ground, especially in environments that have little power. If you're really worried about the Chalices, you might wanna put a Hurkyl's Recall in the SB.