I appreciate all the advice!
Here's what I am doing for 2 reasons: 1) money, 2) nervous about what else may be wrong. I have repaired the gearbox and inner engine with new gaskets and the shifter shaft. However, because I haven't heard the bike run and have no idea what else may be wrong, I am going to reassemble with a new timing chain and gaskets. I pulled the filter basket out of the frame and inspected it. No particles of any kind. The oil filter area also looks fine (I'm going to use that filter for the first oil warm up then drain/change oil and filter). The top of the piston had no carbon on it, although the two exhaust valves did. I cleaned them. I'm not going to re-ring it or change valve seals or anything else until I hear it run. Even if it's smoking I can at least verify gears, knocks, carbs, spark, etc. If it has issues with using oil, smoking, etc. etc. I can pretty easily take down the top end and fix those problems - in the frame if need be.
The main area I have a concern about is the small end of the rod. it did have a small amount of scoring. I did buy a new piston pin and it seemed to fit ok, but... If it has a knock, i.e. crankshaft/rod or whatever, then I have to reassess the whole project as I probably will have to wait until the 'money tree' has grown more dollars... At least by that time I will have the whole thing reassembled instead of sitting around in boxes and yogurt containers in my garage...
Yeah, I know, not exactly an ideal situation, but I really want to 'prove' the engine before I continue to throw money into it. The bike (supposedly) was running fine when the chain guide broke in two. However, my latest guess as to why it broke is because the chain was worn out and flopping around.
My Scottish roots of being cheap are fighting a battle with my Swedish roots of excellence in mechanical engineering. LOL