I've got a 97 Bonneville SE with the N/A L36 3800 Series 2 with a bad wrist pin in the 1st cylinder. I've been looking for another car with a Series 2 that maybe has a bad transmission or body to swap it with,but I found an 04 Grand Prix with the Series 3. I know they are basically the same engine at the core and was wondering if I could drop the Series 3 into my Bonneville without any major complications.

Yes, this has been done many times. The easiest thing to do is swap all the accessories, oil filter adapter, exhaust manifolds, upper intake with throttle body, and fuel rail with injectors from your car onto the engine.

Be sure to inspect your upper intake manifold for damage where the coolant ports travel past the EGR tube. When this area fails, it sends coolant into the engine. I've filled these ports with JB Weld in the past so I didn't have to worry about it. In the past 15 years I've never read about anyone having issues from blocking these throttle body warming ports.

Also replace the plastic coolant elbow that goes from the lower intake to the tensioner assembly with the aluminum dorman one.

There are ways to get the aluminum upper intake working but it requires an adapter and some external pluming to retain the PCV system.

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95 SLE... a keeper. 241k miles. Low and Slow.
97 BMW 528i
98 Infiniti vq35'd i30: 13.3@104mph, 30MPG Hwy (RIP)
02 Jag X-type
03 BMW M5
07 Infiniti G35s 6MT (Sold)
07 Ducati Monster S2R 800 with DS1000 swap
83 Yamaha IT175K
72 Yamaha DS7: '74 RD250 swap, JL chambers

Info on dropping a 92-99: Here.

The L36 and L26 are practically identical, and you can make them exactly the same by swapping on the H-body accessories as mentioned above.

Another L36 will do just fine as well, and only needs to have a small handful of issues addressed in order to be "bulletproofed"

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-Car Guy Carl
"Penelope" - 2003 SLE - 215k Miles
"Sydney" - 2000 Honda S2000 - 81k miles

I had an '04 GP once upon a time and considered this swap into my 02 SLE however I was considering making it fly by wire as well.... After buying this 03 Yukon that is fly by wire and spending well over a grand to have the wiring harness grounds reworked to keep it from randomly going into "Reduced Power" I am happy that I chose not to go fly by wire... Coincidentally the wiring fix repaired the "Battery Not Charging" message too...

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2002 SLE "Frankenbonnie" 02 engine, 04 transmission, and a 03 PCM to make everything talk. Sadly I know longer own
1993 Suburban Zombie Apocalypse Assault Vehicle (GMC Edition)
2003 Yukon Black/Charcoal cloth 4x4 POW/MIA
2003 SLE Silver/Charcoal (New Acquisition)