I'm going to throw in what I know about these bikes just to increase the knowledge base a little.
For all years of Husaberg from 1989 to 2008, they used only 2 different styles of engine mounting. The more common style was for the pre 2001 non-electric start bikes. This motor mounting style was the same as all of the 2001 to 2008 engines. This means that any '01 to '08 engine will bolt into any frame unless it's an e-start frame prior to 2001. This also means that the early non-e-start engines will bolt into the newer frames.
Then there is the second style of engine mounting - the early e-start bikes. They had the starter on the front of the engine down by the front engine mount which necessitated a different design.
How do I know this?
I had a 2000 FX600E and got in a head-on collision with it. The frame was bent at the steering head so I purchased a 2003 frame off of ebay. The engine wouldn't fit because of the e-starter so I sold the engine. I also had a '95 FE501 non-e-start bike and it looked like the engine would bolt right in. It did and I was rewarded with a great handling and super lightweight 500 cc thumper.
Then, the transmission locked up on the 501 and I found what I think is a '97 vintage FC600 engine on craigslist. That engine also bolted right in and I now have a bike that's just as light but even faster! I'm currently setting up a Keihin FCR 40 for it and am super encouraged by the results.
Also, having owned several KTMs during all this time, I must mention that the rear wheels of all husabergs from 2000 to 2008 (not sure about the early bikes or the 70 degree bikes) will swap with KTM's of the same years. This is nice because the 'Bergs had the chain on the opposite side compared to the KTM's and if you're blessed enough to have one of each, you can swap wheels between the two bikes to maximize the tire life. Run a tire on the 'Berg for a while until it starts to wear, flip it around, and run it on the KTM with fresh edges.
04 GO!!!!, 08 KTM 250 SXF (now a 300, now for sale), '07 Beta Rev 3
Frankenberg (98 600 motor, 00 boingers and plastic, 03 frame)
'08 Husaberg FE550 (superior V to R bike), '68 Yamaha DT1
'72 Bultaco Alpina 250 (Mom's old bike)