Yikes, if the intakes were open and the cylinders exposed to the elements, then I think you need to take a close look inside the cylinders to make sure you don't have any rust or any critters in there. You may have to take the cylinder apart...
Check out my project thread for pictures from when I ripped my engine completely apart. Just to get an idea of how much work it is. If you do tear it apart, I highly recommend getting the Haynes manual as well as referencing the FSM. Haynes has some key info that isn't in the FSM.
For the carbs you can visit the wall section and find Radare's great carb cleaning guide. Again, check for corrosion on there too.
SECA II NEEDS ALOT OF LOVE
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Nelsonmd
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NelsonMD's 92 XJ600 Project Thread
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2002 Suzuki V-Strom 1000 (gone)
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NelsonMD's 4Runner Build Thread (Rusted out)
2002 Suzuki V-Strom 1000 (gone)
2004 Vespa ET4 (sold)