There can be dozens of places that a tick or knock can be generated.
Eliminate the external 1st.
headlight, speedo, mirrors.... everything that's bolted on.
and check for rocks in the hub caps syndrone.

Internal to the engine, can be worn cam journals, worn rockers, excessive piston skirt clearance...

And I wouldn't worry to much about smoking on the initial start up, any work will leave something somewhere.  Even washing it will.  If it don't go away or there's obvious leakage then it's time.

So no one out there as had a ticking noise (as if the cam chain tensioner was loose) but knowing it's not the tensioner?   I rebuilt the engine, new tensioner, new gaskets, adjusted valves... all sealed and double, triple checked and still a ticking noise...     Any help?     Thanks

it smokes from the top of the engine, near the exhaust.
The ticking stays the same when it's warm.  
The ticking speeds up with acceleration.
The ticking sounds like its located up top, if I put a little tension with my finger on the cable of the decompressor I can feel the knock.
It does not at all feel like it's coming from the anywhere else then the top near the valves.    
Any Idea?
Thanks so much by the way.

Putting your finger on the decomp cable will give you a sensory input from the exhaust valve...  "feeling it",.. is normal...  (you just put your finger on the valve,... that only tells you, that the bike is running)...

Ticking,.. is an ambiguous symptom...

This is a big, air-cooled, thumper...  they do tick...
You can't compare them to a water- cooled, multi-cylinder...
Air-cooled engines have no water jacket to insulate noise,.. and, valves have looser tolerances to account for more heat expansion...
... and one big cylinder, has bigger valves than a multi-cylinder bike of the same size...

Bigger valves,... less sound insulation,.. looser tolerances for more heat expansion...
= noise...

This could be something bad...  or not... ...
Take these factors into account,... and you decide...
If you can find someone experienced with big thumpy's to give a listen,.. that could be comforting..

I'm not trying to blow you off... Honest...
..but, there are some worriers here...

... ( I have a friend,.. every time I'm in his car,... he says... "Can ya' hear that?"... "can ya' feel that vibration?"...
... and I say...
"Yeah,.. that means the engine's running"....)...

We need to find out, if  you're hearing a problem,...
... or a "Thumper"...

it smokes from the top of the engine, near the exhaust.

robrob,
Unless you are burning off some lubricant on exterior surfaces, the smoke would bother me. An exhaust or compression leak or just lazy smoke? This might be a tough one since you rebuilt a lot of components. Just guessing but I would identify the source of the smoke and see if it leads you anywhere.

The first thing I did after buying an S40 was to buy ear plugs. The thing sounds like a bucket of bolts kicked down a metal staircase.

Good hunting

yup, everything cleaned up and meticulously reassembled.   Checked and rechecked...   Now, did I measure parts such as the cam shaft? no, as I don't have the tools...