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Did I ruin A great Bass?

It’s not a historical collectors item so no worries.
EMG pickups rock in a Jazz Bass, both of mine have EMG ‘s installed, killer sound.
+1 This.
It's doesn't have any intrinsic collectors value in it's stock original state - no reason NOT to upgrade. If you're worried about the battery compartment in the back, I wouldn't - that's actually a plus in my book if I were looking for this particular model. I could revert it back to a true passive if I really wanted to, but as a prospective buyer, it's nice to have that battery compartment already put in as an option.
 
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In 2003 I purchased a brand new CIJ Geddy Lee JB. Has the " Limited Edition" neck plate.
I bought a set of active EMG's and took it to a local luthier / tech and asked him to do the install. All went well , EXCEPT .... When I got it back it had a battery holder installed in the back of the Bass.
In his defense , he did call me , but I was at work and busy so I misunderstood him when he said something about " battery access ".
SO, now that I have a modded CIJ GL JB. Is it still worth what a stock one goes for these days?
BTW , it is a total tone monster and I would not put the stock pickups back in it even if I still had them. It's not my daily driver but works great with my old ME 50B for open mics and jams that I don't want to take my G&Ls and main rig to.
Opinions , comments , and chastising welcome :)
Nope, I did though :) ...
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Absolutely! Original EMG J's with the EMG 2 band preamp is a favorite setup of mine. They were in everything in the '80s. They're not trendy anymore but they still sound killer. The lack of a passive option is the only downside.
Absolutely! Those original EMGs were (and still are) incredible. I’ve got a Jazz with newer JVX pickups and a BTC preamp. Such a great setup.
 
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IMO you didn't ruin your bass, not one bit. You changed it's pickups to make it a better bass for your needs. Rock On!!

FWIW In the early 90's, I bought an early 70's Jazz disassembled in a box. It was a basket-case and I bought it for next to nothing. I had a local guy refinish it, install a Badass-II bridge, new tuning gears and install a set of EMG-Js. It ended up being my #1 gigging bass for over a decade.
You made a player's (not collector's) grade bass better for you, that's all that matters. No worries!
I had a similar situation as quoted above, I found my 72 Jazz in 1993. It was a steal because it had been stripped/refinished and had EMG J's in it. That was exactly what I wanted, anyway. Take a look at what's going on under the pickguard: all those extra screw holes and the crude battery compartment! No big deal, it plays and sounds amazing. I added the Badass II and Hipshot Xtender back then. After the first 10 years of ownership and a TON of playtime, a set of Bart 9J1 and an East J retro was dropped in. Love this bass, it's going nowhere!
enhance
 
You made a player's (not collector's) grade bass better for you, that's all that matters. No worries!
I had a similar situation as quoted above, I found my 72 Jazz in 1993. It was a steal because it had been stripped/refinished and had EMG J's in it. That was exactly what I wanted, anyway. Take a look at what's going on under the pickguard: all those extra screw holes and the crude battery compartment! No big deal, it plays and sounds amazing. I added the Badass II and Hipshot Xtender back then. After the first 10 years of ownership and a TON of playtime, a set of Bart 9J1 and an East J retro was dropped in. Love this bass, it's going nowhere!
enhance
Looks like you have a termite problem. :)