I just did this exact same swap a few weeks ago on my 98 GP, the engine was from a 96 bonneville, so I can answer this pretty well.
You will need to swap out the front engine mount bracket, the rear exhaust manifold, the ignition coil bracket (there's also a stud that needs to be removed CAREFULLY with an e-style [inverted torx] socket from your old engine, and there's probably a pan head torx bolt on the new engine, below the front cylinder head by the water pump, this is a bracket for the ignition/motor mount).
Coolant hose connectors for the heater hoses should be swapped out, the ones on my engine were 90 degree bends from the bonneville, and straight out from the GP engine. Those aren't a parts-store part, so be careful - also, replace the rubber o-rings when you get them out - they are secured with 8mm bolts.
AC pump brackets will need to be swapped out as well, there's (I believe) 18mm and 15mm bolts holding it in - these are a PITA, even my impact had trouble removing them.
While the engine is out, it's a good time to replace the valve cover gaskets as well, and take a look at the rocker arms and valve springs - replace or tighten any parts as necessary.
I really wish I had documented the process a bit better, I could do an entire 5 page write up on this engine swap. I also wish I had taken more pictures, so I could have something to share with you as well.
Unsure on the 99 model year bonneville, but on the 96 bonneville I had to swap out the O2 sensor (I just left it in when I swapped the exhaust manifold). The knock sensors might also be different, but they're a self-grounding sensor with one wire, so if you have the connectors that came with them, you can just splice the wires together and bypass the plug.
Also, the oil filter adapter neck needs to be swapped out, since the one from the bonneville engine will hit the passenger side CV axle if left in there.
The O2 sensor bracket will need to be swapped as well, that will come out with the exhaust manifold.
The (vacuum modulator?) on the front side of the intake (right above cylinder number 3, by the fuel rail) will need to be swapped as well, since it didn't come on the bonneville motor in that same location.
Also, the alternator bracket type thing on the rear of the engine between the intake and valve cover will need to be swapped out, that's the long black metal rod looking thing.
Keep in mind, everything on a vehicle is put there for a specific reason, so if something looks different between the two engines, it should probably be swapped.
In my particular engine swap, the junkyard was rather careless about removing the engine, and EVERY SENSOR was broken, so I had to swap out more parts than I would have cared to, but it ended up working out in my favor because I made some intake manifold/EGR changes and I know I have good, working sensors and fuel injectors on my new engine.
Good luck with your swap, if you need any help, feel free to PM me and I'll see what I can remember. I probably forgot a thing or two in this post, if I remember anything else I will definitely let you know. I just swapped my engine within the last two weeks (end of March, 2014) so it's still fairly fresh in my mind.