Ok, I'm not clear on this. Dosen't the cover come off and then you can dig the seals out of the old cover ? It sounds like you left the covers on the heads after the bolts were removed ...

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I reused the stock seal also. Squirted a bit of red atv on to hold in in the groove. And ditto on the screw seals. Without 'em you'll be spraying 15-50 synthetic all over you legs. Warning: getting the sucker off can be a bit gnarly. I ended up removing the ignition coils to get a bit more room. And wrapped the back end of the chrome one in masking tape so as not too scratch it when working it into place. Well worth it though. Had 3 compliments on it on my first ride out last Saturday. One more thing - be sure not to over tighten the cam cover screws. Stripping the threads out is not unheard of...I think they can be torqued to 10nm.