Unfortunately, the two things you are specifically asking about... helmet and shorts... are two of the most individual-specific items to buy. With the helmet, you need to try different brands because they all have a little bit different shapes and your head will most likely feel best in a certain brand. For example, my head shape fits Giro best... now within that brand I have a lot of options. Every helmet is required to meet a standard. The pricier models do not protect your head any better. What they do is give better ventilation. So, once you've found the brand that fits your head best, then you can determine how much money you want to spend to keep your head cool.
Shorts, again... very specific. Some brands fit one body-type better than others. You need to try them out. Unfortunately, that means you may spend some money finding the brand that is for you. I find that Louis Garneau and Assos shorts and bibs run a little more snug that other brands. Remember when trying them on to simulate riding to make sure the waistline is comfortable (lean over in them, etc.). Sore butt is included with the price of gaining time in the saddle. No matter what you wear, you'll be sore for a few weeks when first starting out. Nothing to do with saddle and everything to do with conditioning. Don't assume a pair of shorts is not good out of the gate - wear them in, use some chamois cream if necessary and then decide after a little bit.
For your tools, make sure they are metric - the hex/allen set you'll want at least 4mm - 8mm as the most common sizes. Remember that the Ruby is a carbon bike, so you don't want to make adjustments on anything that touches the frame without a special torque wrench. You can over-torque and break the frame.
Good luck with the new bike. I'm sure you'll feel like you are flying on a road bike. Though, don't make the novice mistake that one road bike will make you faster than another. Within just a small margin, once you are on a road bike, you'll be just as fast on one as you will be on another. Road bikes are not in and of themselves fast... YOU are fast. Find one that you feel most comfortable on, even if that is not the brand/model you want the most. Happy riding!!