I read through the service manual for both the 2003 Boxster S and the 2005 Boxster S and still have the same question regarding the TTY bolt.

The service manual is vague on setting cam timing on an engine where the timing had already been set. It tells you how to set timing on a fresh rebuild, it tells you how to check if timing is out or not, but it doesn't tell you how to correct timing on an engine that was found to be out. If it is suggesting that you need to rebuild your engine, or pull the engine out to reset timing, that is absolutely absurd.

Car is running 100% now.

A few weeks ago I had successfully drilled out the broken bolts from the heads and reinstalled the exhaust system.

And yesterday I completed the re-timing of the passenger side head. I used the 987 style camshaft tool set and followed these steps (disclaimer: don't follow my steps, or do so at your own risk):

1. Rotated crank pulley until cams were aligned.
2. Realized they'll never be aligned.
3. Rotated engine around again and stopped crank when intake cam was at TDC (aligned with the flat on the head).
4. Placed cam lock bar in the end of the exhaust cam.
5. Loosened exhaust cam bolts and rotated cam forward until it was parallel with the flat on the head (and the intake cam). This was easy because the exhaust cam was almost at TDC and had no significant amount of spring force from the valves resting on it.
6. Locked both cams in place.
7. Installed intake cam locking bar and loosened intake cam bolt.
8. Rotated crank forward into TDC and set the locking pin. Note that I didn't remove the tensioner. Since the intake cam was initially too far advanced, the crank was not yet at TDC, so I was able to advance the crank forward while keeping the proper chain tension. Basically this is like skipping a few steps in the factory procedure - essentially jumping to the point after you install the tensioner and then advance the crank from U60 to TDC.
9. Removed intake cam bolt and installed new one.
10. Torqued exhaust cam bolts.
11. Torqued intake cam bolt to 38lbft.
12. Removed cam lock bar.
13. I also removed the TDC pin because I was afraid of placing excessive strain on the timing chain during the angle torquing step resulting from deflection in the cam adjuster holding bar (/reaction arm), and I was confident that the 38ftlb step would restrain the intake cam adjuster so that it wouldn't move during the rest of the process.
14. Fitted intake cam tightening bar thingy.
15. Completed torquing by rotating bolt 110deg.
16. Removed bar thingy.
17. Rotated engine around several times, verified that cam lock bar and crank lock pin fit, and they fit perfectly.
18. Checked other side head using above procedure and it was perfectly timed too.
19. Reset CEL.
20. Test drive.
21. Success.

Hopefully someone from Pelican reads your helpful description and incorporates it in their Instructions.
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ANYTIME YOU READ ANYTHING ABOUT PELICAN+IMSB +SET-SCREW - check here before you get in the expensive and time-consuming mess that B6T did.

There ought to be a sticky on the forum re this topic.