Thanks ScuRoo for the message, thought it would be nice to give an update from my project
Everything is back together, and the bike (seems) to be running great. It turns out it was the pushrod button that had fallen out causing me to not have a clutch. As I mentioned in my post, the heads seem to have been ported in a previous life so I didn't need to do that.
All of the modifications and work that's been done to my Le Mans are:
Megacycle 620x9 cam, Roper plate, cleaned the carbon buildup on the pistons/ head and valves (and re-lapped them), ported heads (don't know who though), new rings and gaskets, K&N pods, Mistral headers and crossover, and Staintune exhausts from a Guzzi Daytona.
I kept the original valves, springs and pushrods, though I would like to find some chrome-moly pushrods at some point. The ECU is stock to my knowledge. It did have a dyno-jet, but I took it off as the engine fumbled between 1.5-3.5k RPM, though I may but it back on and play around at some point.
My goal from the beginning was to give the motor a refresh and add a little more power without sacrificing reliability.
I seem to have done that; it pulls harder and faster then before and is intoxicating to accelerate out of a corner. I haven't had it on a dyno, don't know who (if anyone) in the Bay area has a motorcycle dyno. I've only put about 1000 miles on since the rebuild so long term reliability will remain to be seen, though I think issues might be due to my own meddling rather then something wrong with the parts/ modifications.
I'm very glad it's so easy to work on the Guzzi! For the most part, a decent mechanics tool set can get most of the bike apart, and parts (including the specialty tools) are surprisingly available online. I would just add, make sure ALL bolts are properly tightened! I've run into so many issues with loose/ loosing bolts because I was so exited to have the bike running again.