I can't speak for the JTV 69 (yet) but I prefer slim Ibanez necks and shark-tooth inlays and I was able to fit one on my Variax 300 with great results.  It's hard to find a 22-fret, square heel Ibanez neck.  Most have the AANJ (all access neck joint) with an angled cut, and all of the popular Ibanez RG necks have 24 frets.  The solution is the Ibanez "EX Series" guitar necks from the early 90's (Korean made).  If you watch, you can sometimes get the whole guitar used for close to $100 (usually a little beat-up) and that way you get all the hardware too.  I had to plug and re-drill the holes, shim the neck-to-body angle a little, and remove the string locks from the nut.  Action and intonation were easily adjusted.  That was my first attempt at a neck transplant and it wasn't too bad.

I recently did a nationwide search at used.guitarcenter.com (no "www") and spotted an EX Series.  I nabbed it so I can "Ibanez" my JTV 69 sometime, but I'm not in a hurry.  The JTV neck is pretty nice as-is.  I called the GC sales person and asked about the details of the neck and action ("Just a few dings".).  It cost $109 and they charged $9 to ship it about 200 miles.  GC "used items" have a 30-day satisfaction guaranty and you can return them to your local store for a refund.  It doesn't get any better.  The guitar arrived in a few days with a nice original hard shell case (surprise bonus).  GC had rated the guitar "3 stars" which was about right because it had paint chips and scratchy pots, but the neck was a keeper.

I bought my Variax 300 for $250 the same way a couple of years ago.  So that's my plug for Guitar Center's used equipment deal !

LIne 6's warranty policy is a bit stringent. I don't see how changing necks or pick ups would effect electronics but in their eyes pretty much anything voids the warranty.

In fact they used to require bringing guitar to a service center in the state it was purchased in. I travel a LOT for work. One day I was in North Carolina in a hotel a block from GC.

I bought a Variax 600 spur of the moment to use  as a beater guitar. A pezo died almost imedeately and I had to pay for the repair at a center in santo domingo where I live. Later on I would get intermittent cutting out and brought to service center in texas, again would have been a charge for repair but the tech was cool. He had it for months and could not fix it, so he didn't charge me. He then said he would never work on variax again. . . . . .lol.

Good point, and it's true the only modification is to the new neck.  I appreciate Line6David's reply though that they would discuss and be fair.