1:  The bottom-most primary cover bolt, if I remember right, in the transmission case 1/4"-20 and on the nut side 1/4"-24. 

Stripped threads there is very common, most because the hole is filled with crud and the stud is threaded in too short, or the nut jams on the stud, or torqued too hard or/and the stud is repeatedly screwed in and out. In short, the threads are easily stripped.

There are several ways to repair this, but to do it good it usually require taking the gearbox out.

A very common mistake is to drill the hole through and insert a helicoil, but then you risk to have a constant oil leak as oil migrate through the threads, fill up the channel for the bolt in the covers, and leak through! the nut threads to the outside. Been there, done that.

In fact it happens also on other places than there. It can be very tricky to find out a small oil leak behind the nuts or through the threads when that is the case. I tape good a piece of towel paper anywhere on suspect (more than once on unsuspected) areas and go for a ride, the paper never lies.

Another way is to machine the hole with an end mill, not through but bigger and thread that with a bottoming tap. Then make a custom bolt with a larger thread at the end. The original hole is 13mm deep, but because of the shape on the inside, the larger hole can't be drilled more than 10mm deep or it risk to break through. Remember that if you opt to use a helicoil or similar thread insert.

Next is to drill through and put in a threaded plug, make the plug of tough  aluminium that has similar expansion rate as the gearbox and have the outer thread dimension as large as possible with a tight fitting in the threads, that produce lesser strain per thread area, and glue it with strong thread locker. Of course the plug has a dead end thread for the stud. There is some distance inside the gearbox until it touches the cluster gear so the plug can protrude a bit in order to make a longer thread for the stud.

Best is to drill out and weld the hole shut, drill and thread a new hole.

At last, the hole cleaned and the stud can be glued in place with construction glue, epoxy reinforced with mixed in aluminium dust.

2: Tried to remove my magneto. Buy 3-4 cheap spanners, cut, grind, bend them so you can grip the flats in different positions, sometimes it is just 1/16th turn before a new spanner with another positioned grip is needed...then throw the bolts and use bolts with 12 grip bolt heads or fabricate bolts with smaller heads than standard. Buy 6-7-10 other spanners and cut and shape the same for the, to put it mildly, infernal front cylinder base nut there...that's the one - right there! Oooh, how infernal that one is...! 

Ps. Make a dedicated puller for the magneto gear. 

If the bolt for the transmission cover is the only reason for remove the engine and only repair you need to do, then in fact I would leave the engine in the frame and resort to the simplest method and try to glue the bolt in place. Reinforced epoxy is astoundingly strong but good preparation is key for success. If it is just the bolt for the magneto, the engine can be lifted up even turned a bit with the front mounting spacers removed, for better access. The gearbox frame fastener nut has to be really loose.

At removing the engine, the problem is the chain cover and in some regard the kicker. The wheel must be removed before the chain cover can safely be removed without scratches and bending. With a rearguard without the hinge, it is difficult to remove the wheel even when the tire is deflated. The lazy way with the wheel and engine in place, 'someone' told me it is still possible to pry out the chain guard forward with the kicker tied down but it is reallyreally tight. Really.

With the wheel out it's difficult and I think risky to lay the bike down so you need to put that wheel back again. And frankly it pose another danger to damage the engine cam cover and fins with the bike lying down. But if you don't have the strength for the lift, that is the way you have to do it. It is doable but I haven't tried that. Remove the fragile carb for safety's sake. The engine with gearbox weigh 50 kg (110 lbs) pretty precise. I think that was without magneto.

Warning. The clutch cover can become indented if the engine is laid on, or hit on the clutch lever worm. You can check if the cover has been damaged from for example a bike tip-over at some time, the flat surface where the worm is should be flat, not concave. A indented cover is problematic as the clutch worm release range is compromised.

With the kicker and brake pedal simply tied down in the right positions, technically it is not difficult to lift the engine out especially if the tank is removed (and that darn chainguard). Just lean the engine toward you a little bit and lift it out. There is plenty of room but you need to have the strength for it. I have always lifted the engine out from the right hand side of the motorcycle, maybe I have done it wrong and the chainguard can stay when lifted from the left side, in fact I don't know! Ah, then you have the clutch pedal in the way...and the shifter.

A block of wood under the engine prevents the engine tipping forward and front cylinder to hit the frame when the front long bolt is removed. Put padding on the front frame tubes and cloth on the bottom rails for good measure.

Good idea to check ite engine over. If you come upon problems, it's better to take a moment and ask before you do something, here or on some of the very active Facebook sites where good tips and tricks can be had from experienced Indian motorcycle mechanics.

Thanks to Carl-Erik's tool advice and Harbor Freight, I was able to get all of the mounting bolts removed from my magneto.  I thought it would just pull free from the engine - but no luck.  New guy question.  What do I need to do to remove the magneto from the engine?

Thanks,

John

The Shop Manual has been very useful to me, as have some of the WoW articles and past postings to this forum.  In the old days, guys like me would have apprenticed to a master mechanic and learned by doing.  I can't thank you all enough for helping with my newby questions.  Especially Carl-Erik who freely shares his time and expertise to keep these great old machines alive.  And all the way from the land of my great-grandfather to boot.  Thanks!