Last year I lowered my Mk6 Transit and although I know its not the new Transit the leaf spring rear strut front set up is still similar and I found some firms who may be able to help
I lowered mine using a spring kit from a firm on ebay who supplied new completely flat leaf springs with new bushes and a pair of front coil springs for about £400. The company is
http://www.wheelmania.co.uk and traded under the name of Vanmania on ebay I think.
Now the problems I encountered were the coil springs were too short for the front shocks and rears had about an inch of travel!
Now I called GAZ shocks living in Ipswich they are only just over an hour away and these guys are amazing, for less than a £100 a side they took my old strut put in their own stiffened short up rated insert.
For the back they made me two shortened damping adjustable from soft to really hard for just under £100. I also fitted a pair of new cut down bump stops for the rear chassis rails which came to about £20 from my local ford Dealer.
Now what I would do if I did it again and I probably will soon as I'm looking to get a Mk7 as the tin worm is starting to win with mine
1. Get GAZ Shocks to re-work my standard struts with shortened inserts, adjustable spring platform and springs, I've known them do this for older cars.
2. Fit new flatter profile leaf springs with cut down bump stops, this is quite simple and doesn't involve flipping your axle. I carry 200 - 300 kg with no problem. The only problem is I don't know where Wheel Mania had the leaf springs on mine made.
3. Have GAZ Shocks make up a shorter set of rear adjustable shocks
Now I'm sure the above could be applied to the New Transit Custom, it cost me all in about £800 to lower mine, but a phone call to GAZ could definitely lower the front and I'd be very surprised if they don't have an answer for the rear, when I was there they had an area of their workshop all full of bespoke suspension struts.
I'm not sure how to add pictures if there is a simple way to add pictures and someone can explain it to me I'll take some pictures of mine to show all of what I have just wrote is not bullsh@t!!
Good luck lowering your van honestly try GAZ I'm sure they will be able to help