As the engine has hydraulic valve lifters, how was the rocker shaft re-installed? The issue with the loose shaft bolts near the allegedly misfiring cylinder are interesting, but probably NOT the reason for the misfire on that cylinder as I suspect the stiffness of the shaft would keep things as they need to be.
Replacing the valve guide seals, on the engine, if done properly, should not have caused any issues either. I've heard of no issues resulting from such a labor operation if done correctly. Main thing is to ensure the valve stem keepers are all put back so that they are fully seated on the valve stem and the spring keeper is engaged with the locks correctly, to me.
Putting the rocker shaft back onto the cyl head has some issues, especially with hydrualic lifters with oil in them. When the engine stops, not all of the valves are in the same place. Some open, some closed, or anywhere in-between. When the rocker shaft is removed, the plungers inside of the lifters will extend, even if they were compressed with the shaft installed. When the shaft is re-installed, those plungers have to be re-compressed to their prior position. We know that fluid will not compress, so the shaft re-torques have to be done in incremental steps, to gently re-compress the plungers.
On an engine with adjustable hydraulic lifters, as a small block Chevy or others, when adjusting the valves with the engine running, the procedure is to back-off the adjustment nut until a "tick" is heard (space between the end of the pushrod and the rocker arm), then slowly tighten things back down until the click is gone (zero pre-load) and then tighten the adjustment in no more than 1/4 turn preload segments. Done slowly, the particular cyl can "miss" as the lifter plungers are moved against oil pressure. After a few strokes, they compress and the engine runs smoothly again. If NOT done in small doses, PUSHRODS can be bent.
Additionally, if the specified torque sequences are not followed, with the shaft being the main intermediary item between valve spring pressure and the hydraulics of the valve lifters, the shaft might become a bit "tweaked", too, in the re-torque process. Yet, to me, the pushrods are designed to be "a weak/sacrificial link" in the valve train. Strong enough to do the job they need to, but also the first to "give" to prevent other damage, if needed. Easy to replace, too. With no other issues which might be at play, that's what I would check.
Just some thoughts,
CBODY67