@MtyQuinn - Drilling is
EASY. (I believe the location is different than this Gen I write up on newer models) Use
Stat-O-Seals on both sides of the tank and it won't leak, ever. You can get these in various sizes from many sources. Hydraulic hose shops often keep them in stock or you can buy them online.
Pegasas is one online source. A good thread sealing compound is also a good idea. I like
Loctite 567 thread sealant for fuel fittings like the bulkhead fitting. Note that it needs a lack of oxygen to cure, so any excess outside the threads will not cure and is easy to clean up. It's fuel proof as well. I've installed three different bulkhead fittings with this and Stat-O-Seals with somewhere around 350k miles of use w/o any trace of leak or weeping. I am a retired machinist that worked in the hydraulic tools division of Stanley Works. I used lots of different thread sealing, locking, retaining, filling compounds, including near daily use of 567 and know it's properties well.
Some important things to know with any fuel cell project - Keep the fuel line from the aux to the main tank as low and strait as possible. Try not to go up and over an obstruction. I drilled some holes in the plastic under seat tray to allow a straiter run, for example. Do install an inline fuel filter off the aux tank. A clear plastic disposable one, not a glass one. Vibration can cause the glass ones to come apart and leak. The clear plastic filters allow an easy visual check of both fuel flow and debris in gas, which can provide a clue or even an early warning if you get contaminates in your fuel.
@Greg Rice - Please report back when you go places for bonus points, under conditions that you didn't choose, especially in the West where distances are more vast and a rally bonus can take you far off the beaten path. Burning up the interstate is a good proof of concept in fuel flow, but lacks the variables rally conditions can cause. And I do also wonder if you've ridden in extreme heat with that set up yet. That's a common condition for vent line aux cell issues.
Every single person using the vent line method can tell you stories about having no access to aux fuel and being unable to fix it during the ride. (Ask the Lehmans about their IBR and the Africa Twin aux fuel issues.) Your turn will come, if it hasn't already. On the FJR if you have no vent line for the main tank and have issues with your vent line aux set up, you run the risk of several negative problems, the least of which is starving the bike and having it stop running. There have been imploded tanks in the worst case scenario I can think of with vent line problems. The more common issue is a vacuum in the tank that doesn't allow the gas cap to open or just no fuel feeding from the aux tank. On a bulkhead system you can deal with it, should a problem arise. Usually quickly.
At the end of the day it's a personal decision driven by several factors. Choose what works best for you.