Not knowing the tractor you have, how does the pto engage? Do you engage it manually with foot clutch or hand control lever or is it electrical engagement where it engages in a shock fashion. IF you engage it manually, can you not rev the tractor up to rpm speed and slowly engage manually so there is no shock to the system. The other quesion is your tractor does not have a 1,000 rpm and the cutter is 540 do you? The pto shafts should prevent you this happening due to difference in groves.
I am with others here who say never engage at full pto rpm.