Ducati 996 or 748 to 999 engine swap!

Back in 1999 I fell in love and bought my dream machine, the Ducati 996. With the years going, by the power on the track and on the street just doesn't cut it anymore. Don't get me wrong, in a curve it still slices the new liter bikes in to pieces. The power was to low to keep up on the straight away. So it was time to build up the motor. With reseach I found that I could buy a used 998r. So I'm thinking engine swap time. A motor with a great balance of power and torque for the Desmoquattro chassis would be the 999. Here's a rundown of the 999 series motors:
The 2003 999 bip and mono and s were the same motor as the 998.
The 2004 999 bip and mono were the same as the 02 998.
The 2004 999 s had upgraded cams (2001 996R/2002 998R) and deep sump (only certain models not all in us)
The 2005 bip and mono had the deep sump and the "R" cams. Now I am not sure about The 06 but i heard there were no changes except the R. All of the R's had light components and even different bore and strokes so those are different machines. The desmoquattro frames would either require moving/modifying the cross member because the link bars that hold the two separate throttle bodies together interfer. However this is except for the 996R(which is a 998) and the later 748R models that came with shower injectors. The frame is the same however slightly lighter but actual geometry is the same as I have had both side by side 998/748r/748. The motor itself will fit 998/999 powerplant into a desmo frame. As far as wiring goes if you opt to stay with the older wiring harness 1.6m then stay with the old radiator and one fan. Unless you want to start cutting and adding your own connectors on the harness and fans. The 998/999 use two less sensors. The 998 does not have the sensor on the top of the water coolant expansion tank and a temperature sensor is removed and plugs with an aluminum blue plug you will also need to get the 998 radiator hoses which are slightly different. The 999 uses a metal tube which is part of the case so that would have to be changes or get custom hoses made. The sprockets are different as the 996 has two bolts and a plate and the 998 has one large bolt that threads onto the shaft. Ok back to the wiring if you are switching to the 998 harness then you will have to change the starter solenoid as well because it is a different connector, the spark plug wires are different and the front part of the harness is about 2" longer. The sensor under the head light assembly is different as well as the mount. The battery tray is different to support the ecm which is mounted near the battery and moves the starter solenoid slightly also the turn signal flasher unit is different as well as the way it mounts.

The air boxes are different. The 748-996 use the same, the 748R's with shower injectors came with a much larger box, the 998 is somewhere in the middle. The injector systems are different. The 748 has two direct injectors (one per cyl) while the 996 has four direct injectors(two per cyl). The 748R has aluminum shower injectors that are suspended by two metal rods, two injectors shower type (one per cyl) non machined version of the RS, the 996R and the 998, 998s, 998R all used the same throttle bodies and injectors which are shower type but suspended from the venturies. This is why the aftermarket air filters are different. The 999 shower injectors are very similar except the fuel hose is slightly different in the way is is routed and there is only one cross member instead of two. So you might have to change that segment of wiring depending on the changes.