This post has been a long time coming but I feel it will be useful for those of you who are going to or have thought about doing this swap. I will include the total costs of the stuff I used for it. All the new parts came from Advance Auto Parts unless noted otherwise. Once all the parts are gathered the swap can be done in a weekend if you're by yourself or if you have a friend or 2 with you, probably in a day. You will notice that very little fabrication work was done on this project. I used parts from other vehicles to simplify and speed up the process. Also I don't have much experience making things so it's probably for the best!
First the parts:
NEW
Boss clutch kit for a Samurai $70 ebay(yes a stock Samurai clutch has held up well for my 98% street application)
Samurai flywheel $50
Bosch Fuel Pump part#69100 $99 w/lifetime warranty
Purolator fuel filter part#F63169 $9
Mazda 323 GTX distributor cap $27
Swift GTI rotor $9
Electric radiator fan $70
30a switch $5 Wal Mart
48" universal performance radiator hose $60 ebay
2" Thrush Turbo Muffler $20 Summit
2" free flowing catalytic converter $60 Summit
Cheesy chrome resonated exhaust tip $9 Summit
90-93 Accord cold air intake $13 ebay
universal MAF adapter for cone filter $10
Used Parts:
Swift 1.3 DOHC engine and harness $700 Aftermarket4x4 (Heckuva deal I think)
Sidekick 1.6 16v tubular steel exhaust manifold $100 Aftermarket4x4
Swift MAF meter $35 MNSamurai
Sprint thermostat housing $15 MNSamurai
Samurai Tach cluster $45 Ka4yqi
80's Ford truck external fuel pump mount $5 U-pull it
91-96 Escort fuel filter mount $5 U-pull it
Fab Work
Modification to the harness $450 Trail Tough
Speed Sensor Modification $85 Trail Tough
Exhaust Manifold machine work $30
Exhaust plumbing $140 Sharpsburg Muffler
Total $2121
I will not go into to much detail about how to remove and install the engine as it has been covered many many times. I will say that I used the stock Samurai engine mounts and did not hammer my firewall in any way and it fits ok. Also the Samurai transmission bolts up perfectly and the Samurai starter was also used.
Engine Modifications:
Once you remove the engine it's time to swap over the Samurai oil pan and pick up tube to the GTI engine. They will be a direct bolt in replacement of the Swift pieces. Make sure your pick up tube has the o-ring on it. I had to bend the mounting brackets on my pickup tube because they came in contact with the crankshaft. I just bent them until I could turn the engine over without it hitting anything. Now swap out the GTI water pump pipe with the Samurai one. Either get a new o-ring for it or be really careful with the old one. I'd recommend using some kind of lubricant when pushing the pipe back in the water pump housing so that the o-ring slides in where it's supposed to, otherwise it'll leak. There will be one extra opening on the Samurai pipe that you will not need. Cap it off. Now is also the time to put on the Sprint thermostat housing. There will be a large extra threaded hole you will not need so cap it off as well. It's the one in the center.
Ignition Modification:
I used a fairly simple set up for mine. A Mazda 323 GTX cap and a stock GTI rotor. Looking at the 323 cap you will notice it has no spring loaded center brush. I drilled out the 323's center brush deep enough for the center brush with the spring from the Samurai cap to fit in it. Again be careful doing this. I did it a little at a time until it was perfect. The reason I chose to do this instead of putting a spring on the rotor was simply because I didn't want to mess with anything that moves. The rotor is spinning pretty fast in there when the engine is running and I didn't want to risk anything vibrating loose. The cap ends up looking like this when the engine is in. The only thing that touches the firewall is the little dust cap as you can see.

Fuel System Modifications:
The stock fuel filter was used as a screen for the new pump since the pump is only high pressure on the output side. I used the famous Ford fuel pump due to no fancy connections and plentiful stock at most part stores. It is mounted to the underside of the body using the mount from an 80's Bronco that is made for this same pump. It has good insulation and fits perfectly with the pump. You can't hear the pump when the engine is running. The power wire is ran down the transmission tunnel using the factory bendable wire holders along the way to keep it in place. It is grounded to the speedo cable bracket nearby. Make sure you have the pump oriented in the right direction. I did mine backwards the first time only to hear bubbles blowing in the fuel tank the first time I turned the key on. The pump set up looks like this.

The filter I used came from a 91-96 Escort due to the same reasons as the pump. Also the Escort mounting was used. I put it just underneath the intake manifold on the passenger side. It looks like this.

People have asked me why I put it there. It's easy to get to. It's close to the engine so stuff has less of a chance to get into the rail and that's where it was on the Escort!
Exhaust:
I used a stock exhaust manifold from a 1.6 16v Sidekick. This one in particular was tube steel and not cast. Using the GTI exhaust manifold gasket as a template you will see that most of the bolt holes line up perfectly already. Some of the holes you will not use because the GTI doesn't have as many studs holding it on. I had a machine shop drill out the ones I needed to use to make it fit. Once you get that part taken care of you will have to cut 1" off each of the runners where they mount to the head flange in order to get clearance from the steering shaft. Also the egr bung will have to be closed off with the welder. Once the mainfold welded back together you can clean it up and throw on a nice coat of high temp paint! Purty!

Wiring:
I looked to Trail Tough for this. The harness came back labeled for an easy installation. All I had to do was use wire taps to connect them to the existing wires. Mine matched color for color. The speed sensor was also plug n play. There's a single yellow wire that connects it to the modified harness. Everything else plugs in to the stuff under the hood. The harness was ran into the cab from a spot pretty close to where the factory ecu was. I used a 2" hole saw to carefully drill out a spot for the harness to go through. You will need to use a 2" grommet to keep the sharp edge of the new hole from rubbing through the insulation of the wires. I got one off a car at the junkyard. The hole is here:

Cooling:
The stock radiator is being used with an aftermarket electric fan wired to a manual switch inside the cab. The 48" radiator hose was used because the thermostat is on the opposite end of the Swift engine. I also used a small piece of the stock upper radiator hose to connect to the 48 incher due to clearance. It was the only way I could think of to get it to work. The stock lower radiator hose fits perfectly when using the Samurai water pipe. Here are a few pics. Pardon the coat hanger hose bracket. I had to use something to keep it off the exhaust manifold!


Intake:
I used the cold air portion of a cheapie Accord intake with a HKS filter I had laying around from another project. The pipe had to be shortened quite a bit but it seems to be doing the job.

Other odds and ends:
The brake booster line had to be flipped upside down and bent a little to work with the new engine. The stock temp sender wire and oil pressure light wire will have to be used in order for them to work correctly. Make sure you remove the factory ecu. The Sensor light will stay on if you leave it in.
I'm sure there are little things I'm forgetting but I'll be happy to answer any question you may have if I can.