Wire up a 5.9 FI Magnum to 60's A body.

I can't speak for the '99 in particular, I don't know if it has a separate body control computer that it needs to talk to.
Earlier ones were just a matter of 4 or 5 wires to hook up for basic function, beyond that (say you want to have the OBDII plug wired in under the dash for diagnostics, or wire in a CEL) would be additional. The JTEC PCMs are pretty straightforward, it's not like hacking the new hemi computers. Programming is available through anyone with SCT Tuner's Suite. You may have to run some T fittings and double up on some sensors to keep your dash readouts.
For transmission control, you'll have to dig up the schematics in the service manual and invest some time and beer deciphering that.
Someone like @TT5.9mag may be able to help with other particulars.