Many thanks to Doug and Carlos at www.Vortexmotorsport.com for their help with this engine swap project. More to come...
Finally the 996 3.4 engine arrived! Before it was crated I had the company that I purchased it from install a new IMS bearing set (the latest Porsche version of the bearing that shouldn't fail). This should be good insurance for this engine.
I plan to give the important details here about the transplant of the 3.4 into the 2.5 Boxster. Already I can tell you that the people that talk on the forums saying that it is "plug and play" don't know what they are talking about. The first thing that I noticed when I compared the two engines was that the throttle body on the 996 is on the wrong side. Also, the wiring harness is not the same and it appears that I'm going to have to pull the entire intake system off of both engines and swap over the harnesses. I haven't even gotten to the exhaust yet, but I already know that the O2 sensors are going to be an issue.

Here is the 3.4 996 engine as it arrived in it's crate. The engine has about 40k miles on it and came out of a wrecked 1999 996.
Here is the top of the Boxster engine with the wiring harness disconnected as well as other hoses, wires and tubes.
Here is the inside of the rear trunk with the inner panel removed and the wiring harness already pulled through to the engine compartment. The ECU has to be removed to accomplish this.

Porsche sells a special tool to support the engine during this process. We made our own special tool out of two 2X4s and a good chain and it worked just as well. The second picture shows the drive shafts disconnected as well as the exhaust removed.

The engine is finally out of the car! I jacked the car up as far as I could to get the proper clearance to pull the engine out. You can place a couple of 2x4 pieces under the drive shafts and wedged in the suspension to get them out of the way so that the engine will clear them. Just don't damage anything wedging the wood in there. The second picture shows the front of the engine as it was removed. The A/C compressor was unbolted and stayed in the car. To accomplish this, the belt had to be removed.

In this first picture you can see the engine compartment as it is without the engine as well as the wood that I discussed earlier to hold the drive shafts out of the way. The second picture is of the engine finally out and ready to be pulled over to the 996 engine to begin the swap of the harness etc.
By the way, I removed this engine entirely by my self. It can be done...
THE START (The latest additions will be at the top of this page)
This is the starting point of my 3.4 Boxster GTR project. Its a 1999 Boxster with a blown 2.5 L engine. And by blown, I don't mean with a super charger! The good thing is that the car has never been wrecked, so its pretty straight with only minor dings on it. It is totally stock at this point, but that's going to change very soon!

The interior is actually not in real bad shape. It will need some work and some nice mods, but the seats are in good shape and there are no tears or cracks in anything that I'm keeping.

The plan for this car is to transplant a 996 3.4 L engine which will give it more than 300 HP. That will be nice! It will also get a better brake and suspension setup as well as a complete Fiberwerks Aero GTR aerokit along with new paint. To complement the new power and looks, it will get new wheels and rubber, but I'm still debating which wheels to get.
This is the car during a recent test fit. Still trying to decide which rocker panels to go with, the GT3RS style or the TA style. Maybe I'll develop some new ones.

This is the new Fiberwerks Aero GTR front bumper that the Boxster will be getting. It will be balanced with the Daytona II rear wing for better downforce in the rear as well.
I'll try to keep this page updated often with progress notes and pictures...