How much difference if the tonearm is mounted 5mm

Weather it will have any effect will depend on the length of the slots in the head portion when the cartridge is mounted. Their slotted for a reason. 5mm is only 2 tenths of an inch. Not much. Most slots are quite a bit longer that that so if using the recommended mounting distance would have placed the cartridge in the center or even forward of center of those slots, you just might not have a problem.
Regards.

As Griffithds said it will depend if you have enough room in the slots of the head shell to compensate for the distance lost.

Also if you use an arc protractor it will need to be one that is for use at the same pivot to spindle distance as you have mounted your tonearm at. Otherwise it will be way off. What type of protractor are you going to use?

If you are mounting the new arm in the stock VPI hole then I doubt it will work. The pivot to spindle distance for a JMW-9 is 223 mm. Which is 9 mm longer than your new arm. That's very unlikely to work.