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Not trying to be insulting, but did you put the vacuum caps on the new carb holders? Ed

That's okay, 650ed. I'm new to motorcycles, so all advice is welcome. But my carb holders don't have vacuum nipples.

Well I guess vacuum caps aren't a problem. I should have looked at the carb holder diagram before I asked. Ed

lack of vacuum is definitely a clue. I guess a compression test would be in order now, too.

I tested compression in both cylinders. Nearly identical numbers -- 142 lbs. I pulled the spark plugs, stuck a soda straw in cylinder #1, and turned the crank. When the cylinder reaches the top, the fixed timing mark lines up with the T mark on the advancer. So there's nothing wrong with the way the advancer connects to the crankshaft.
Maybe it's the rotor, but it really doesn't look as if the "slug" has moved. Maybe you're right, loudhvx -- it's the wrong rotor, and the timing was always off. Maybe there are multiple reasons why the bike runs so rough. I'm sure the carbs need to be synced again. Or maybe the rotor lobe knocked the pickup coil upside the head, and now the pickup coil isn't working properly. I'll try re-positioning the coil I've got now. I'll have to drill a new hole in the mounting plate. If that fixes the timing problem, then the pickup coil is fine, and I just need to re-position the slug on the rotor. Loudhvx -- I might contact you for that. If that doesn't fix the timing, then I guess the coil must be bad. I'm not going to find another one soon. I'll look for a parts bike, and in the meantime, I'll consider switching to points. I found an old points-type advancer from a 1980 440, and "georgefix" on ebay has all the other stuff I'll need.

The strange thing is, if the pickup was hit, but is not visibly altered, then it doesn't explain how the rotor can be lined up with the pickup and the T mark simultaneously, as in your photo. For that to happen, something has changed with the physical relationship of the rotor and/or pickup. Any internal electrical fault won't explain the physical change. However, my experience is with inline-fours, so there is a very slim chance the twins pickup work on a different principle, which may explain the physical alignment difference, but since they are so physically similar, and since both can use the same igniter, I suspect they basically work the same as the inline fours.

You probably already know, if you go to points, you should get a new 4 ohm coil.

Keep us posted.

I drilled a hole in the pickup plate and moved it where it wants to go. No change -- the bike still idles rough and stalls. I tried to adjust the idle speed screw and pilot screws, but that didn't help. I tried to check the timing, but the strobe was flashing intermittently at best. Sometimes not at all. That was happening the other day too, when I first tried to re-position the pickup. I pulled a plug to see what kind of spark I was getting. Intermittent, weak, with an occasional nice, fat spark. When this problem first began, I was getting good spark all the time. The plugs are black from all of this cranking and not running. I'll clean them up, charge the battery, and start fresh tomorrow.
Points are looking better and better.

I tried to check the timing, but the strobe was flashing intermittently at best.

That's your problem, if it won't flash the strobe you have an ignition problem, likely a coil / ht lead/ plug cap issue. Assuming your strobe is ok, get this working first, then check timing. Also clean up/replace coil terminals. Until you can strobe the ignition timing you can't really go any further.

Dodgy ignition usually manifests itself at higher rpm, if it won't even light a strobe at idle then you certainly have a problem.

Getting somewhere now, good luck and stick with it.

So then you most likely had the timing issue all along, but clearly something else had changed. I agree with Tyrell, you will have to get the ignition operational before setting the timing or fixing the other problems (if there are any).

Did the coil get wet? That can make one go bad if it's old. They develop cracks over time, but work as long as they stay dry. As soon as they get a good drenching, they will start to fail.

If it's the igniter, though I think you replaced it, if I recall, you can make one very cheaply. The details are in my signature.

I've had the bike in my garage all winter, so it's never been wet. And just to be clear, when the bike started running poorly I still had good spark. The timing was off, but the spark was strong and regular. Over the last two weeks, I've disconnected the plug wires several times while doing resistance tests, so I thought I should make sure the wires were connected properly. (New 7mm wires and caps from Z1.) I cleaned all the connections with that electronic spray cleaner stuff, trimmed a half inch off the ends of each wire, and reattached them to the coil and the caps. I put in the freshly charged battery, and now I have good spark again.
With the pickup plate moved to its new position, and with good spark, the bike idles better. It wasn't great, and it stalled when I tried to rev it, but it idled long enough for me to adjust the speed and pilot screws. Not much change there. When I check the timing, I'm still not on the F mark, but I'm really close. Just need to move the pickup a little bit more. BUT -- when I turned the screw that syncs the carburetors, suddenly I had good vacuum on carb #1. Still no vacuum on carb #2. So, as you guys guessed, there is more than one problem at work here. I've had the carbs off several times to clean them and adjust the floats. They were fairly clean to begin with, and back in February I added new o rings, new float needles, new pilot screws, cleaned the brass parts with carb cleaner, blew out the passages with compressed air, and adjusted the fuel levels with the clear tube method. But I'll pull the carbs off and check everything again on the weekend. Maybe, last time I had them apart, I put something in backwards or upside down.

It shouldn't affect the idle position, but may affect vacuum... have you checked the slide diaphragms for holes?

Over the weekend, I cleaned the carburetors for the fourth time. I didn't notice any blockage or anything installed wrong. I put them back on, started the bike, and I have vacuum in both carbs now. I wish I knew what I did to make that change, but I'm not complaining.
I got a second advancer body in the mail. I found it on CL for twenty bucks. Unfortunately, it doesn't include the rotor, which now seems to be the piece I really need. But I noticed something about the weight arms. On the advancer I got in the mail, there are little pads (magnets?) on the arms that touch the cylindrical part of the advancer when the bike is idling. I think you can see one of them in this photo.



On the weight arms from my original advancer, there are no pads.



I don't know if they were there before and fell off, or if they were never there at all. At any rate, I put the arms with the pads onto my advancer body, lubricated everything, and put the advancer back on the bike.
With the pickup coil in its normal position, my timing is still off. With the pickup in the new, adjusted position, the timing is right on. After a little tinkering with the carburetors, it's running good again. I could leave the pickup coil in its new position, but it's only being held there by one allen bolt. Also, it's blocking a clear view of the timing marks. I think I'd rather correct the rotor. Or find another rotor.