i asked this qn few yrs back, and thus sold my J-custom and now im only left with a Suhr modern.
my modern is a basswood, maple top, maple neck and pau ferro board comapre to standard J-custom with maho body, maple top, maple neck and rosewood board.
Both guitars have very good quality finish. But i do not know does both uses the same dying methods, what i can tell is the poly finish on the modern looks alot thinner than that on the J-custom. The maple top use by Suhr definetly own any standard J-custom top nowadays.
Having said that, the J-custom has the bling factor of vine inlays which will set you back alot if you were to custom it on a Suhr.
Both guitars have excellent fret work, although the ones on J-custom looks nicer with rounded edges and neck binding, just some cosmetic stuffs. The fret ends on the modern feels good as well, and of cause you have the options to choose whether you want them to be SS.
Neck fitting: Base on these 2 guitars, i will say the modern has a better neck fit into the pocket, there is a slightly bigger gap on both side of the J-custom, and for those who are particular about neck fit, and tone transfer/vibration etc etc between the neck to the body, J-custom has a rounded end neck heel, thus will not have full contact with the neck pocket and the modern has a square heel which will has full contact with the neck pocket.
Neck Profile: I always thought Ibanez wizard profile are the perfect shape for my hands, but after playing the thinner modern profile, it definetly fits my hand better. I can only describe it as being not so wide compare to Ibanez wizard, but is a little bit thicker, which allows me to grab the neck better. I bought a modern without trying as there is no dealer in my country, was worried about the neck profile initially, but now i know the modern neck fits my hand better, you should try it out to see if you like it.
2 main factors which makes me decide to sell the J-custom are the neck profile and the sound coming from the Suhr. I know both uses diff wood, but the Suhr resonate more and i find the clean sounding of the Suhr is alot sweeter and clearer compared to the J-custom, im not sure if its the work of the pickups or bodywood though.
And from doing some readings online, i read that maho body will sounds nicer with a maho neck compared to a maho body with maple neck. Maybe something you would like to look into.
Hope these infos help =)