I have a 3300 as well and agree with Hook. The most important thing it to throttle down before shifting. You can do it at full throttle but it puts a lot of strain on the GST. You should not use the clutch to shift while mowing as the pto stops when you use the clutch. Use the GST and shuttle shift.
I have been running my L3300 on biodiesel for two years with no problems. I started with a 50/50 blend and now am using 80% bio. I go back yo regular diesel in the cold weather. I have had no problem with the fuel filter.
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It just takes a little time to get used to how to do it. Make sure your pto is well greased (tractor and shaft ends). Align the shaft with the pto and turn either the shaft or the pto until the keys in the shaft align. I find it is usually easier to turn the pto. Slide the shaft partway onto...