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BIKE will not shift pass 2nd gear . I have 1st neutral and 2nd that it. I am at a loss. Need all the help I can get. I don’t know if fixing it is an option or buy a new bike. I have a lot of money and time into my 2004 1300C
 

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2002 VTX1800R Lowered 2" Rhinehardt Flush Cut, Brown County X with Flames Air Box Cover
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How long you owned bike?
Have you done any maintenance?
Have you looked in VTX1300 Tech Board?
Here is a link for you for starters.
 

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BIKE will not shift pass 2nd gear . I have 1st neutral and 2nd that it. I am at a loss. Need all the help I can get. I don’t know if fixing it is an option or buy a new bike. I have a lot of money and time into my 2004 1300C
If you plan on trying to fix this yourself, the first thing to do is become familiar with how your clutch system works. Ideally you will have an owners manual, and even better would be a repair manual to familiarize yourself with.

Here is the owners manual, if you don't have one. How to adjust the clutch begins on page 99:
http://owners.honda.com/assets/ownerlink/model/own_man/powersports/2004/2004_vtx1300c.pdf

Since the gear shift process involves a clutch cable, and proper tightness of the cable to properly move the clutch so the gears can shift, one of the first things to check and ensure is your proper clutch play adjustment. This is explained in the manual, but I've also attached a video that might help:


Someone in another post suggested It may help to remove the engine side cover to lube the ends of the linkage pivit points.

This link below explains various reasons a motorcycle my have gear problems:

Motorcycle Gear Change Problems & Solutions (Explained)

Note: Since our bikes oil also lubes our clutch make sure your oil levels are at full, and you should have the recommended oil in your bike to avoid shifting issues . Make sure to use oil that is formulated with anti-shearing agents and additives for buffering gears and is not energy conserving. The Honda manual suggests:

API Service Classification SG or higher except oils labeled as energy conserving on the circular API service label, SAE 10W-40, JASO T 903 standard MA, Pro Honda GN4 or HP4 (without molybdenum additives)

Keep us posted on your progress.

Good Luck! (y)
 
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Shifter pedal pivot point needs clean and lube . I am not concerned, very small amount of movement on the turnbuckle link ends. One other recent 1300 had shifting issues. He broke a fork. Probably abuse...
 

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As above, did you check your shift linkage at both ends, tight, appears nothing recently moved, clamp tight and teeth on shaft not stripping. Get the back wheel up on jack or stand as below and run it thru the gears. I've run mine up to 100mph on the jack but you don't need to, it will shift nicely thru the gears at idle.
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BIKE will not shift pass 2nd gear . I have 1st neutral and 2nd that it. I am at a loss. Need all the help I can get. I don’t know if fixing it is an option or buy a new bike. I have a lot of money and time into my 2004 1300C
Based on what you report; my guess is #6 is loose or #19 has broken.
The shift from 1st to second has the greatest amount of travel.
So in my thinking that eliminates the external shift linkage and/or connections, as the problem.
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