The distributor or coil shouldn't really be clicking

If your battery is low or you have bad connections you can get that clicking of the solenoid.

If that's the case, charge the battery and clean your connections at the battery, the solenoid and the negative cable connection to the engine block as a place to start.

When you turn the key to Start, does the engine turn over with the starter or just click from wherever?

Don't forget to clean your battery terminals also, sounds like it could be a bad battery connection.

It sounds like your tranny shift linkage may not be in sync with your throttle linkage.  You could just disconnect the tranny shifter cable at the transmission and leave it loose until you sort this out.  Manually shift the tranny into the center lock position, you can feel the ball detents engage at Forward, Neutral and Reverse.  Test all three and make sure it is seated in neutral.  Then try your key, the engine should spin.

 As far as your clicking sound, are you sure the dist cap is properly seated and the rotor inside is not hitting the cap as it turns?  There is not much there than can click.

You seem to have 2 unrelated issues, first the neutral safety switch/shift cable adjustment and second an ignition issue since when it's turning over, it won't start. 

When it's turning over, have you checked for spark?

PS ............you've e mailed me pictures before (your broken damper plate issue), so e mail whatever you want for this problem if you have questions on the distributor brand etc)  And if you don't still have the address it's keno439@gmail.com 

Sounds like an engine that has no spark or no gas.

Told him to check for spark and try priming it with a little shot of gas down the carburetor being careful to watch for a backfire out the carburetor.

Like he said earlier and the video also showed, it turns over with the shifter in forward completing the circuit through the Neutral safety switch, the relay/solenoid isn't his issue

The distributor has a Prestolite electronic module in the original Prestolite clip down cap distributor.

No but.............he says up above that it only "clicks" when the shifter is in neutral and he turns the key to Start  (maybe an electrical arcing noise?)and the starter has no power, but when he moves it to fwd, turns the key to Start and the misadjusted cable lets the NSS feed power to the sol/relay and the starter, it turns over making normal turning over noises. 

So I didn't hear the "click", maybe it's there but covered up by the noise of the starter and the rotating but not starting engine.

Kinda "weird"

I'd post the video but it might take me a year or so to figure out how 

I would trust KENO’s nose and troubleshoot spark and fuel first.  2-3 tablespoons of gasoline down the old carby has worked well for me.  Be sure to replace the spark arrestor first.  I’m putting my money on spark problems.

JQ

Here's some reading and a video that should help you out Reed

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=26601&title=shift-cable-adjustment-pcm-123-and-morse" rel="nofollow - link  to cable adjustment thread

http://www.youtube.com/watch?v=9KNzQxpAeE4" rel="nofollow - link  to video

PS.............what did you have to do to get the engine running?

JQ

Here's a picture of a Holley inlet seat partially screwed in (orange arrow)

The yellow arrow is pointing at the plug you have circled in your picture. You don't want to mess with that plug unless it has an external leak.

You access the internally adjustable needle and seat by taking the float bowl off and removing the plastic baffle, the float and it's spring 

Here's a slightly fuzzy picture of what it looks like if you take the bowl off and hold it upside down 

The white baffle slides out to access the needle and seat after the float and spring are removed.

Use the container because it'll spray out the line and surprise you and make a mess too if you don't use the container 

Since the boat originally ran for you, I'd check the pump before tearing into the carburetor.

If you're gonna tear into the carburetor, do yourself a favor and get one of the many Holley carburetor tuning or rebuilding books that are on the market.

Here's a link to some examples

http://www.google.com/search?q=holley+carburetor+book&oq=holley+carburetor+book&aqs=chrome..69i57j0i22i30l9.20394j0j4&sourceid=chrome&ie=UTF-8" rel="nofollow - link

They all have their good and bad points, but the David Vizard book is probably one of the better ones

You could be stubborn and crank it longer, with a piece of clear tubing on the suction line so you can see if any gas is moving at all.

If it doesn't pump, a pressure gauge won't do you any good.

You probably have a Carter pump. The Carter number is M60389, you can find them for a wide variety of prices on line

Or you could get in touch with Then and Now Automotive in Weymouth and get a rebuild kit or have them rebuild what you have now.

The newer ones aren't rebuildable, the older ones are. Their rebuild job will be more expensive, but seems to use better parts than the newer pumps

Send me pictures if you want to verify what you have for a pump 

Here's a link to Then and Now

http://www.then-now-auto.com/" rel="nofollow - link

Reed    Your fuel pump is an AC dual diaphragm marine fuel pump, the green arrow points to the place where you can hook a hose to that would run up to the carburetor/flame arrestor to indicate a ruptured primary diaphragm. Somebody has a black hose hooked to it.

It's a lot easier to see fuel in that line if it's clear 

That line being clear vinyl is OK per the USCG regs and speaking of the USCG regs, rubber fuel line between the pump and the carburetor is perfectly acceptable as long as it has the right rating and the hose clamps are clamping the hose onto barbed fittings. The hose is rated USCG A1-15 or a later version is A1-10. You won't find it at your local car parts store.

Here are a couple of links you can read

http://www.uscgboating.org/assets/1/AssetManager/ABYC.1002.01.pdf" rel="nofollow - http://www.uscgboating.org/assets/1/AssetManager/ABYC.1002.01.pdf

https://www.gpo.gov/fdsys/pkg/CFR-2011-title33-vol2/pdf/CFR-2011-title33-vol2-sec183-558.pdf" rel="nofollow - https://www.gpo.gov/fdsys/pkg/CFR-2011-title33-vol2/pdf/CFR-2011-title33-vol2-sec183-558.pdf

CBR1000 dude should probably read them too, it's been gone over many times here on CCF.

Some people like rubber, some like metal, the Coast Guard just tells you what they approve.

And for your other question..............yes a plugged fuel filter could be your whole fuel delivery problem, but the stuff plugging it had to come from the someplace like a dirty gas tank.

More pictures of the engine would be good.

I've had 4 CCs and all had metal fuel lines, and thought it was standard. Routing of rubber fuel line so close to high heat sources and spinning belts, moveable dog house engine cover, also seems dangerous to me. Just my opinion of course.

I got 3 out of 4 right side up ..................not too bad 

I think all 79 Commander engines came with the AC pump and a rubber supply line from the pump to the carburetor as original equipment.

It may not have the USCG stamping on the hose, but being hose that's about 43 years old, I'd probably replace it........... just because.

The flame arrestor has the right fittings for the breather hose from the oil fill cap (big fitting) and the ruptured diaphragm indicator clear hose The carburetor also has a fitting for the fuel pump overflow hose and it looks like the black rubber hose mentioned earlier is hooked up there. Just pick one fitting to use and cap the other one. No real advantage of using one over the other.

I think I'd put the carburetor back on, new filter, hook up the fuel line, prime it with a little gas down the carb primary throats and see if it starts and runs, then do things like replace the hose and if necessary the fuel pump and/or a carburetor rebuild.

Let's cross our fingers and hope it runs and your fuel supply issue was the filter being plugged.

Then you could also change the fuel filter/water separator on the suction side of the pump to make sure that isn't a problem, 

And then the line from the tank to the filter/separator could probably also use replacement if it's original 43 years old, and the anti siphon valve on the gas tank could be checked too.

I guess you could call it a pretty original "survivor" 

If the rusty coil is working, "then don't fix what ain't broke"

If you have ignition issues, a coil replacement might be in your future

Here's a good thread to read in the link below that might help you decide if you want to tackle a stringer job.

I think they started out not knowing a lot about stringers fiberglassing etc. but did a heckuva job and it's well documented

http://www.correctcraftfan.com/forum/forum_posts.asp?TID=40614&PN=1&title=new-to-me-78-tique" rel="nofollow - link

Figure out how long you think the process will take and then multiply that by 3 or 4 and you'll probably be close