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Jackson Bass... many issues...

I could describe my bass but it'd be quicker to show the model directly from the site

http://www.jacksonguitars.com/products/products.php?group=CBass-Body&page=1&product=2909000385

I have the blue model and it is one of, if not the most, comfortable bass I've ever played. 24 frets, lovely action, beautifully adjusted.

My biggest problem is with the tone... it's not the kind I'm really into, I guess. Maybe it's not versatile enough, especially with my amp, but I think it lies mostly in just being the wrong sort of sound. As far as covers go, I play mostly Rush, Primus, and other prog and funk stuff... And my pickup layout just doesn't sound right for it. I make it work, but most other basses I've played sound better.

I'm all for replacing them, which brings me to the second issue. It's really hard to do work that requires woodworking on a bass that has no pickguard to cover it up, and it's not angular in the slightest, all smooth curves, so putting on a pickguard would be difficult. I also really am not a huge fan of the blue thing, I'm more of a red guy... but I would really prefer a natural wood tone bass...

Add this to the fact that the input jack is on the side, something that allows it to twist and turn, leading to an excursion with solder to repair every couple months at most. And I'd love to put a kahler tremolo on my bass, but people keep warning me I might ruin it.

So, the obvious solution would be to get a bass better suited to that sort of thing, but there are two problems with that... one, the fact that it's a wonderfully comfortable bass, and two, that I'm a poor college student who can't really afford another bass.

The next simplest solution would be to try to cut open the bass and make all the modifications I want, but I'd end up with one ugly instrument, and I'd probably resort to short cuts and settle for things that aren't really what I want in order to make it as easy as possible and avoid scarring the instrument.

The final way I could try to fix this is take the neck off and try my hand at making a bass body, one that more or less matches the balance and weight of my current one. This would be difficult but probably would end in the most final satisfaction. Problem is, I have no idea where to start, as this requires all the same decisions and skills as the second answer, and then some....

So I would happily accept advice from anyone who can address any of these issues, singularly or together.
 
I agree with the "deal with it until you can afford to get a better one" advice. It may be comfy, but there are other basses that will also be comfy. An option to consider, once you have about $500-$700 saved up, would be to have a luthier like Mike Dolan custom-make you just a new body, with the appearance and hardware you want, and he can carve it to match the existing body for comfort.

You may also find that a different string set, and some careful use of EQ, can get you dramatically different tones from the bass you already have.
 
That looks like a standard PJ setup, and there should be some excellent aftermarket pickups that might get you the sound you want.
Starting with new strings, per Bongo, is prolly your best bet.
 
Changeing the pups to something better suited to you does not require modification. Theres plenty of pup upgrade options for PJ basses. Dimarzio, Seymour Duncan, EMG, as the main big name pup brands that come to mind for this. As to problem with side mounted jack. Thats the most common position for input jacks. What are you doing to yours to cause damaging the jack? Change the ouos to the Jazz & P pups that you like the most. And your sound problem should pretty much dissapear unless soapbar/humbucker type bass pups are really better suited to your sound. If your not too familiar with the diff PJ pups out there, Dimarzio's std PJ bass pup set has been a fave for many pros and amatuers for more then 30 years.
 
swap the pickups with something else, and think of possibly installing a preamp.. as for the output jack.. loosen the jamb nut on the jack itself, then put a drop of clear nail polish on the threads, then re-tighten the jamb nut.. the jack will not come loose, until you want it to.. and start using 90 degree (L shaped) jacks, with the cord going over the strap lock.. this will prevent many problems with having a side mounted output jack.. most of my basses have them..
 
I have the blue model and it is one of, if not the most, comfortable bass I've ever played. 24 frets, lovely action, beautifully adjusted.

I'm all for replacing them, which brings me to the second issue.

Add this to the fact that the input jack is on the side, something that allows it to twist and turn, leading to an excursion with solder to repair every couple months at most.

And I'd love to put a kahler tremolo on my bass, but people keep warning me I might ruin it.
I have the blue model and it is one of, if not the most, comfortable bass I've ever played. 24 frets, lovely action, beautifully adjusted. << for what it is yes. I like the pointies more than the gumbyheads but that's me :D...

Add this to the fact that the input jack is on the side, something that allows it to twist and turn, leading to an excursion with solder to repair every couple months at most. << I have plenty of side mounted jack basses and NEVER had one loosen up on me EVER once you put a drop of nail polish on it like throbgod said if it need it.

I'm all for replacing them, which brings me to the second issue. <<< no issue, the OEM electronics plain sucks and you should have researched into it a little more for tonal qualities to what you like to hear out of a bass but they do sell a ton of replacements and they are standard p/j so no cutting or routing is necessary.

And I'd love to put a kahler tremolo on my bass, but people keep warning me I might ruin it. << ruin what? I have many friends who also have one mounted and never did any of them cry that it didn't work properly....
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I own a lot of Jacksons so I am pretty knowledgeable about them but like the others are saying, if you hate it, wait a little bit and sell/trade it for something that comes out of the store the way you like it or yes, you will buy another one and perhaps STILL mod it to your liking :)