I know what you mean I had exactly that problem after an engine teardown. Although that Gunsmoke method is well written and widely used, it falls down if you want to make sure everything is ok before hitting the starter. By make sure, I mean you zipped tied the camshafts but didn't realise the crank sprocket deep down at the bottom had moved!
Have you got the Clymer and oem shop manuals? Make sure you haven't mixed up the exhaust and inlet camshafts. The manuals tell you how to tell the difference and how the slots on the end of the shafts align, but the biggest problem for me was 'visually judging' they were horizontal to the cover surface. You could easily get a tooth out. I seem to remember cutting a piece of steel to fit in those slots.
The next problem is making sure the crank is set in the correct position to start with because you cannot see the marks behind the timing cover and they are on a very small diameter so not that accurate anyway. That is the position at which the number one piston is at its highest point (Top Dead Center). In the engine combustion cycle, the No.1 piston is at the top on TWO occasions. You want the one when the plug will be fired.
With care you can poke a cocktail stick into the No.1 plug hole and 'feel' the piston coming right up to the top. If you turn on the ignition switch, the correct piston being fired is the one when the fuel pump just whirrs. Curiously that corresponds to the firing point. But remember this occurs just before (figure in manual) the No.1 piston reaches the TDC. For setting the cam sprocket markes, that No.1 piston needs to be a little further on and right at the very top.
So now you know that the crank is rotated to the correct part at the start of its cycle when No.1 piston is at TDC when it would normally fire and all the marks on the camshaft sprockets should align, as per the text and photos in Clymer.
There are some things to watch for:
Once the crank is set for no.1 piston at TDC it may move but probably won't if you are careful. You should pull the chain hard up against the bottom crank sprocket but not so hard it turns. There is no easy way to lock the crankshaft. Some say they can do it through the rear wheel on the stand with a timber wedge under the tire, but there is a lot of lash in the driveline. The best way is to remove the right hand engine crank cover and slip in a shaped piece of timber between no. 2&3 crank journals and the casing. I have another little tool I made which is a long length of rod I can thread into plug holes of the pistons sitting at Bottom Dead Centre, that holds the crank solid. Fortunately, in these engines the plugs are central over the cylinders.
The cam chain will not be tensioned on the back. You must always turn the engine crank in the normal direction of engine rotation which keeps the chain tight on the front slope. The correct positioning of the bottom crank sprocket and the two camshaft sprockets with all marks correctly aligned is with tension on the front of the chain loop and the rear slack.
It is quite difficult to determine No.1 piston TDC with a cocktail stick. This should really be done with a micrometer clock gauge and an adaptor made from a drilled out spark plug. There is another method I have used a lot. You drill out an old spark plug to make an adaptor for a small bore hose (6mm) or find a hose fitting the same thread as the spark plug. Attach a length of clear plastic hose formed into a 'U' and put some light oil into it. bring the piston to just before TDC and connect the adapted spark plug. You now have a very sensitive pressure gauge which will help you find the piston TDC without marks. Remember to remove the gauge before fully rotating the crank, else all the oil will disappear inside the cylinder!
When you have done all this, you must rotate the crank several times watching the valve cams and checking the piston positions to make sure the valves are doing what they should in the combustion cycle: Inlet opens on piston down stroke, both valves closed for compression when a fuel pump whirr' should be heard at the firing point TDC, then exhaust valves opening after the power stroke. At no position should you feel the crank lock up as you rotate it.
If that is ok, you can then put the plugs back and start the motor.
The one thing I have a problem with is the alignment of the camshaft slots horizontal to the cover surface. The chain must be under some tension but not so much as you turn the crank sprocket, I used an open ended wrench on the camshaft for that, because there is a tendency without the tensioner for the camshafts to move in the opposite direction from valve spring tension on the other cam lobes. This is when it is best to have the crank locked at TDC. I have used a steel ruler as a straight edge. Don't keep staring at the marks/slots, because they look horizontal anyway after a while! I am fairly sure if you got this far with all the rotation tests ok, a tooth misaligned would not damage the motor. But you might hear it sound different. I used some 12" welding rods fixed to slots in the shafts to make a better judgement of the horizontal alignment. I used the same rods to make an angular measurement of when a valve should start to open, checked against the manual tech. spec.
Sorry this is not so simple, but that is the problem with the zip tie method. OK until something slips.
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