5.3 LSx vs a 5.4L Modular isn't even in the same universe. One makes over 100 whp more than the other, is smaller, cheaper, WAY stronger internals and parts are next to nothing. Just saying. The whole "purist" thing... I can get where that is coming from but it makes 0 sense to me personally. The swap is so well documented these days and especially if you don't have to worry about OBDII testing its not hard. Even if you DO have to worry about OBDII testing you can change the VIN of your swap ECU with EFI Live to match your chassis when they scan it and turn off any DTCs that are present.
Now if we are just talking about a replacement motor to get you by... just get any old 4.6L PI out of a JY and drop that sucker right in. Swap over your accessories and whatever else if its not a whole assembly out of a Mustang. That would be THE cheapest and painless and 100% direct swap to get back on the road.
As far as crankshafts for the modulars, just find a good OEM Cobra crank for a 4.6 and run with that if you are going to build up a 4.6 motor. I picked up a whole Teksid block AND an OEM Cobra crank out of a 98 for $250. If I did go ahead with a modular build it would be Boss rods for $160, $500 set of MMR pistons and, $200 for machine work and $350 for studs and there is your cheap "built" modular 4.6L shortblock on the cheap good for 800hp which is more than I'd ever use on the street but that's me. And then you get into modular heads and cams... those are going to be $2100-$2500 for ported PI heads and good cams or $3300 for TFS with cams. So figure you are going to be into a modular longblock for $5k or so. And still make less power than a $500 LSx truck motor with a cam swap.
Personally, I am STRONGLY considering the 5.3L or a 6.0 LQ4 if I can find a LQ4 for cheap but a 5.3L is a proven beast of a motor and On3 has just released a Mustang/LSx turbo kit for $1750. Motor/cam/intake and a turbo kit for less than the price of a pair of TFS 2V heads and cams. No brainer and just using one of the options I am looking at as an example. I love Mustangs and all, I like the look, I like how easy they are to work on, that the Fox4 platform is nice and light and simple and I like the SN95 interior better than the F body. However, the motors are not in the same league as the Chevys.
""Puts on flame suit""