Just as an FYI, I was able to remove the cylinder head recently by removing all of the engine to frame mounting bolts except the bottom rear. (Just loosen that one to use as a pivot) Once you have done this, loosen the drive belt adjuster nuts/bolts and the engine will tilt forward giving you enough room to remove head. It's a lot of work. You will have to support the bike with jacks because the kickstand has to be removed in order to remove one of the bottom engine mount bolts.

How deep can you run a bolt into it?

You can repair the front-right head cover bolt, and mid-right head cover bolt by drilling through and installing a 1/4-20 grade 8 bolt with a grade 8 nut.  It can be done without removing the engine from the frame.  Do not attempt to do this on the rear-right head cover bolt.  That requires cylinder head removal because the rear-right head cover bolt hole also serves as an oil passage.

This shows a repair of the mid-right bolt.  Just drill straight through with a 1/4 inch bit.  These long bits are readily available at any decent hardware store.

You might have to do a bit of grinding on the cylinder to get the nut in place, but its minimal.  I love this repair.  I actually do it to all my builds now.  It's way more robust than the stock setup.

It will easily handle the factory service manual spec of 6 - 8.5 ft-lbs.  On the 1/4" grade 8 bolts, I go past that a bit.  A 1/4 inch grade 8 bolt should be torqued to about 9 ft-lbs with lubricant, 10 ft-lbs zinc plated, or 12 ft-lbs plain & dry.  The torque wrench is essentially a way to measure the friction in the fastening system.  Lube the threads and you use less torque because there is less friction.

Note: zinc plating is considered a form of lubrication.

The weak link in this system is the aluminum internal threads.  IMO, the aluminum threads give up over time.  The cyclic stress resulting from thermal expansion keeps working at the aluminum threads and eventually they crap out.  Of course, they can also fail if the bolt is overtightened, but a correctly designed fastening system will fail on the bolt, not the internal threads.  That's why whenever a steel bolt is used in an aluminum component, there's like at least double the length of engagement.  I suspect the Suzuki design department has an army of engineers that stay busy all day long doin fastener calcs.  I'm willing to bet they got the design right.  But as I mentioned, over time, the constant increase/decrease in stress as the cylinder and head heat up and cool down fatigues the aluminum internal threads.  Keep in mind that when the stress is highest, the assembly is also hottest.  The yield strength of aluminum tanks at a pretty low temp.

Drill through and put a nut on the bottom and now you no longer have any aluminum threads to worry about.  Even though the length of thread engagement is only about one-fourth of the original design, the grade-eight steel is so much stronger than the cast aluminum that the reduced engagement does not compromise strength.  An additional bonus is if there is a fastener failure, it will be the bolt.  Install a new nut and bolt, rock-n-roll.

With the years of feeling bolts come to their clamping force, I prefer that over a torque wrench in places other than heads and things that have to not leak under pressure.
In this case, the fact that a book said X inch pounds of torque gave him a target Other than the feel of a bolt coming tight. With a thumb on the head of a 1/4" ratchet and using fingers closing to move the ratchet, you can Feel rotation that isn't matched by an increased resistance, which IS what the very first split second of failed threads does. It's possible to Stop there and get away with it. Knowing the next time you have to go in there, you are gonna hafta address that.