Yes it is a major problem but it can be solved.
Basically the 3.15 gears fit into the 5sp t/case same as the auto but the low range gear fouls on the selector rail boss (this is where the 5sp gearlever mates to).
I ordered and recieved a selector rail and boss from Japan and Mark will be looking to make a new version that has enough clearance. The new selector rail and boss will be supplied as part of the 5sp 3.15 kit. With the 5sp you have to drop out the gearbox and t/case anyway and to swap over the selector rail is a simple job just something extra that will have to be done as part of the install. I believe the US never got a 5sp version of the 3.5 V6 so it won't effect them. I'm dropping off the selector rail & boss along with a t/case to Mark on Monday because he wants to rectify this ASAP.