[BRADEY]

My 2003 Electra 350 with Electronic CDI (Capacitive Discharge Ignition) has been a faithful companion for 9 years and has been largely trouble free for over 25000 miles.
However over the last 1500 miles, the peak performance of the bike has come down considerably. As against a very easy laid back cruising at 50 MPH, the bike's egnine seems to feel extemely rough, strained and reluctant to constantly maintain those speeds.

One more thing that I have noticed is the idle, after a short ride. It gets a bit rough as well, with cyclic high and low idle (though on a cold engine its perfect).

Any suggestions on what to check for. I have already ruled out lean fuel mix, as the plug is nice and tan, the engine is smooth up to 40 MPH, so I am not able to understand if there could be any trouble in the electronics, namely the ignition coil, the pick up coil /trigger coil or any other. Pleeeeeeeeeeeezzzz Help I love my bike !!

[Ice]

 In the 1950's it was pretty much expected that these lumps would be torn down and gone through about every 20,000 miles or at least the top end torn down for a good de carbon.

Using a good fuel additive can help keep things clean inside, are you using one regularly ?

 Carbs can and sometimes do develop leaks at the enrichener plunger seat/ seal and occasionally the slide to bore clearance will wear a bit. You might check those if or no other reason than to rule them out as causes of the current symptom.

 How long since the last full and complete service and detailed tune up, oil change and fresh new air filter ?

Modified to correct speeling airors 

[barenekd]

Check your compression, see if you have any rings left.
Bare

[BRADEY]

i wish i could find a systematic guideline from one of you, to go step by step on this issue to nab the culprit 

[Vince]

     Check for an air leak and check for a tight valve. Either would cause your symptoms.

[barenekd]

A shop manual should offer some help.
Bare

[REpozer]

     Check for an air leak and check for a tight valve. Either would cause your symptoms.

Vince is right (again) . Thats about as systematic as it gets. Basically everyone is saying the same thing here.
1) look for vacuum leaks (air or sucktion leaks) . That is sucking air into the air intake side from somewhere other then the air filter.  Commom area for leaks are the rubber intake boots attached to the carburetter.....leaks from rotten rubber or poor fit. Also could be like Ice said a vacuum( suction) leak in the carburetor.
2) compression test . You need a new tool for this . Borrow a "compression tester" from a friend. Do it. Is compression good or bad?

[REpozer]

Bradley, if you don't have a manual, this page was made by Thumper. He did a nice Job putting this information together.
http://mysite.verizon.net/respud62/

Like Vince said, check valve adjustment. ( a tight valve can cause llow compression)