As I've sad I've haven't done it by myself and I don't have skills and needed informations to help you. In my opinion best think you can do now is to use support ticket and contact Line6 with your problem - use this link http://line6.com/support/tickets/add.html

I bought my 59 in 10/2010, got it in 5/2011 -- bumps along the way -- switch issue, but fixed. Saw no reason to change its pups --  they sound very good as they are. Bought another JTV in 10/2012 -- this time a 69S -- 3 single coil pups. Liked the way they sounded except for the single coil hum. I've been a Fender guy and know that's what to expect with SC's, but got spoiled by my LP and the JTV59 humbuckers... So I bought & installed a set of DiMarzio noiseless SC's -- the Injector Bridge, Area 67 middle, & Injector Neck. The install was kind of a pain -- lotsa wires and short leads etc, but I did it fine -- look at the wiring diagram of the new pups versus the L6 document mentioned above.

The new ones sound very good - have some more output the than the L6 originals, but are quiet as a church as far as hum goes -- even quieter than the HB's I have in the 59, my LP, and my 1973 Fender Tele Deluxe -- way quieter than my Strat. I really had no issues with the 69S's original pups' tones, besides the SC hum... Had to change the DiMarzio's cover from white to the mint green color of the L6 face plate & pups on the gold 69S, but that was like $10. Did it after living with the ones that came on the replacements for a couple of weeks, so had to open the guitar up again to do it, but was no big deal. Worst part was dealing with the trem bridge coming unhinged when the strings were removed to take off the front plate to get at the guts. I did ithe pickup swap in January -- not quite 2 months from receiving the guitar. The guitar's been a champ all along.

I know you're talking about the regular 69's HB, but you will probably run into some of the same stuff under the hood that I did. The only replacement I would worry about the pickup levels would be active pups, like EMG's etc that you would need to power with a 9 volt battery, If your target pup is passive, it should not be an issue. The guts are the same in all of the JTV's, as far as I've heard, and the 89's pups are supposed to hotter than the 69 & 59 HB's. From what I recall of discussions here, the 59 HB is hotter than the 69 HB, as they were trying to keep levels somewhat balanced between the 69's HB and SC pups on the same guitar, I'm not an authority on that, just recall it sometime ago coming up in the forums...

They had 3 different versions of the pickups for the 3 JTV's that they had funny code names so they could distinguish which went with what model -- Kirk was the 69, and then there was Bones (59) & Spock (89) -- Star Trek references. When I pulled my SC's out of the 69, they are marked Kirk-B, Kirk-M, and Kirk-N (Bridge, Middle, Neck)... Apparently they still are following that....

For what it's worth -- my 2 cents...

Dave