Parts wise, building a 4.6 stroker motor is actually fairly cheap. Obviously you could buy a kit or complete motor from someone like Hesco, but most of us are on a little tighter budget and prefer to just use 4.2 parts. To build a 4.6, you need a 4.2 crankshaft and 4.2 rods. For reference the 4.0 crankshaft has a stroke of 3.411", while the 4.2 crankshaft has a stroke of 3.895". 4.0 rods are 6.125", while the 4.2 rods are only 5.875". Now you can use the longer 4.0 rods, but then you must use custom pistons. So sticking to the budget build idea, you'll use a 4.2 crank, 4.2 rods, and stock 4.0 pistons. Now the 4.2 rods are necessary to use a stock style piston, however, the piston will end up in the hole 0.008" father than stock. Now milling the block would be the easy answer to return deck height to stock, and fix the quench height problem (Quench height is the deck height plus the thickness of the head gasket. A quench height of 0.035" - 0.060" to prevent detonation). However with the extra stroke the compression ratio is already approaching the 10.1:1 area, so milling the block will increase this problem. Most people typically just leave the motor as is with the piston an extra 0.008" in the hole, and just run premium gas. However using dished pistons, and increasing the chamber size of the heads can help with this, and allow you to mill the block down farther to achieve idea quench height, and still run lower octane gas.
Now there is a problem with the snout of the 4.2 crank, it's to long for a serpentine belt pulley. You can have it cut down to the correct length or use a spacer or stack of washers (obviously have it cut down is the better option).
To prevent lean conditions at higher RPMs, normally the injectors also have to be upgraded. There's all sorts of injectors that you can use, but most people tend to use the 24 lb Cobra Mustang injectors. An adjustable fuel pressure regulator will also help you achieve the proper fuel/air mixture.
Now during the rebuild process you should replace the cam and lifters. If you want to gain some more power from the stroker build you'll want a camshaft with a little more duration. Most of the aftermarket cam manufacturers make a variety of cams for the 4.0. Obviously a header would be helpful as well. 99-up WJ 4.0 intake manifolds are actually worth some power as well.
Before starting a build of this extent, you should do as much research as possible. There are lots of other things you can do here as well as porting the heads, polishing the rods and pistons, etc. Building a motor from scratch is pretty involved, so do your homework first.