Hi 77salisbury, Modern fuel is different than '70s fuel world wide. So old specs may not apply. Non stock mufflers or air filters can change mixture also. I would NOT use top groove. I'd start with center groove. You may find bottom groove is better after road testing & evaluating mixture.
Good you cleaned pilot jet & cleaned passages. What float are you using? The original plastic or the new black stay up with stainless steel needle tab? What needle? Original plastic or aluminum with viton tip? With stay up float it is acceptable practice to bend metal to set level. No matter if you bend or move seat as you did. It's the fuel level in bowl that is what you want to achieve.
Popping on deceleration. What do you mean by popping? A little back fire is most often from exhaust leak up front at head & occasionally at muffler front joint. Any air that gets sucked into exhaust system can ignite unburned mixture & pop. However a blub blub blub on deceleration manly at lower speeds like 30 mph or lower like coming into town easy is too rich mixture. Too lean on decel in my experience sounds normal, like nothing is wrong.
Mixture screw per shop manual is 2.5 turns. However that is misprint. When concentric came out screw base setting was changed to 1.5 turns. So 2.5 turns may put you lean.... However mixture is set at normal idle rpm. If idle is biased too fast it's not the same really. So I'd put at 1.5 turns now. Then correct idle. Then go back & trim mixture & idle again. Remember you want a good warm motor before you do final rpm & mixture adjustments. When idle is correct warm, it will be too slow & too lean with motor cold. That is normal & expected.
Regarding idle. Stating what you may already know, you must have enough cable slack to allow slides to drop to slow idle. After you get idle & mixture at best setting, then go back & readjust cables. Kind of time consuming & a pain. That's what is "tuning" adjusting everything to it's best position. Of course any changes effects the other. So you tune until you get it best it can be. Takes practice, but with practice becomes easy. Still takes time though. Sounds like you are getting there.
Regarding smoke from head, cyl on start up after tear down. I find it normal. Even when trying to clean & wipe down everything, I always see smoke as motor warms. This is with perfect assembly, not leaks etc. I get worried every single time as it smokes. Usually takes about 20 min of running to burn it off. Sometimes more. Depending on cly paint it can stink for several rides. I mean real rides 50+ miles. Next day ride again, stinks again. Took my cyl about 6 long rides to cure paint. Duplicolor Ford semi gloss black heat resistant motor paint.
Regarding oil leaks at acorn nuts, I don't know if it was leaking or not. If leaking, obviously it would smoke. You didn't seem to notice leaking so I expect smoke was just normal start up smoke. 2 miles will only show bad leaks. Small leaks/seeps may take 30-200 miles to show.
I see what you mean on exhaust rocker threads. Does look like end of shaft may have been machined back?? I see repro shafts that have end that looks similar, but I don't think they have shortened threads.
The fat cap on end of rocker shaft is actually separate pressed on piece that can slip on shaft so you can't always go by what you see at left end or rocker box. What you want to go by is the shoulder on the rocker shaft where it necks down. That shoulder should be tight against the right inner wall of rocker box. You can remove valve cover & look in & see this. Normally from factory there is a 3/8" ID washer installed so actually the washer is pinched between shaft shoulder & box inner wall. (some owners modify the washer positions). You'll have look carefully as the thackery spring is covering area.
Back to the pressed on end at left, if it looks good like intake & you see right end is tight against inner box wall, then someone shortened threads.
I don't go 22# on torque on these. It just seems too tight. I do it by feel. I've had practice though. Next time I'll check with torque wrench & see what it reads. I have a little torque wrench with dial reading.
Anneal all 4 copper washers for banjos. Bend hook on end of long wire. Heat washer one at a time on gas stove burner or propane torch to red hot. Drop hot washer in cup of cold water to remove black scale.
Not a bad plan to put some sealant on washers also. Loctite 518 is my sealant of choice, however Hylomar universal blue or any of that family of hylomar will work good also. Put a thin smear both sides. Wipe hole of washer clean. Hang washer on wire 10 min to flash of solvents in sealer. Handle washer from outside. Assemble & tighten acorn nut. Make sure you don't smear sealant on threads or shaft sliding washer on. Clean box surface, banjo sides, nut face well & dry. Sealant doesn't stick well on oily surface. Wipe off excess quickly.
If banjo fittings want to spin when tightening nuts, counter hold them on the flats. Don't let them spin & bend tube.
If... The threads on acorn nuts are still good, you should be able to ride many miles with the old nuts. If threads are damaged, you risk damaging rocker shaft threads. If threads are damaged I'd wait for new nuts.
Tip: thin smear of Hylomar on valve cover & primary gasket works good. Again 10 minutes or more to flash off solvent. Not longer than 30 min though. Seal the copper washers on primary cover the same way.
Regarding head gasket retorque if you rode 2 miles I'd check it now. Generally I start bike & ride it around the block, return to home & check oil return, check for obvious leaks. Don't shut bike off. Smoke is coming from everywhere it seems. I've already suited up ready to ride. I'll ride bike about 2 miles, not babying it, just ride normal. Pull over & look for leaks or obvious problems. Evaluate how bike is running. Often I'll lower idle as I set slide stop screws as a guess, which is usually too high. I'll go another 5 miles, check again. Often will trim mixture screws & idle screws as needed even though motor is not really warmed all the way. If all is good I like to go for a good 30 mile run to heat soak motor & evaluate things as I ride. Now I'll set rpm & mixture. I static set timing with points. With Boyer I can only set by the hole & dot carefully. Never ever lug bike during breaking in. So even if timing is off I'm not in danger of holing piston. After 5 miles I'll go ahead & spin the motor up to 4500 for brief periods. After 20 miles I'll go to freeway & run it 55-60mph. The canyon roads you cannot run this fast. Bring it back home & shut off. Look it over & see what may need more work or if any oil seeps have cropped up.
Next day after cooling all night, I retorque head. Adjust valves. Adjust clutch push rod & lever. Check/adjust primary chain (usually ok). Inspect points cavity to be sure that seal is not leaking. Strobe check timing. In that order. I suit up & take a good 50-100 mile ride. This time I final adjust rpm & mixture. I'll ride bike next day another 100 miles or so. Set overnight. Check head torque & valve adjustment again. It often will take more torque. Valves may or may not need to have screw turned. I'll check clutch rod again. Next head torque & valve adjust will be 500 miles. I'll drain break in oil between 300-500 miles. Check clutch rod at 500 miles also. If new plates used, it takes a few adjustments to compensate for settling in.
There after I'll check head torque every 3000 miles before valve adjustment. I find if you do this after about 6-9k miles the bolts don't seem to take more torque. I mark bolt head & allen wrench with felt pin so I can see where it was & if it goes tighter. I always give torque first to see if it moves. If it doesn't move I back off slightly, like 1/32 of turn, then go tighten direction to torque. Never jerk or too slow pull torque wrench. 1/8 turn per second is a good pull speed. Jerking is the worst. Never do that.
Remove tank to torque head. Don't remove rocker boxes to torque head! Just remove the 4 large bolts that hold rocker boxes on, 5/16 thread. These screw into the allen head nuts. The torque on these bolts is only 10#. This will feel loose with the big head & threads, but use 10#. A light smear of Hylomar blue on the washers is good idea to prevent leaks around washers. Hylomar cleans off easy with some carb spray or brake clean etc.
Forgive me for nit picking, but the kind of clamps you are using on banjo tend to damage hose & seep over time. The original type like factory used are a safer choice over time. They are sold at many auto parts stores or eBay. You can remove screw & open clamp, then fit it over hose so you don't need to pull off hose. This hose is 5/16.
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They come in 3/8 also for the oil feed hose from frame sump.
I have no idea what you want for mufflers. I have stock type Emgo that replicate the originals. They are not loud at all. They are long & ugly though. Emgo makes a 1970 type muffler, but with long front pipe to hook to T140 stock front pipe. They sound a little louder than original 1970 mufflers, but are not too loud at all. Many Emgo mufflers are not very costly. Mine weren't. Overall mufflers are not cheap though. I don't care for loud mufflers, I don't like following bikes with loud mufflers. That's just me though. Loud is the opinion of listener though.
Once you finally get this bike set up, it will be a joy to ride for many years.