That cover is really only there to protect the shaft during shipping. I asked to have my cover so I could install it when I wasn't using the pto, um never have put it back on. No reason to put the bolts in if you don't want to, the holes are at a dead end in the case, but installing them will stop stuff from going in there just in case you fine a use for the bolt holes.
About you RPM... Do you have a "PTO" rpm range (green) on your rpm gauge? I have a 1533 geared trans and what I do is keep it at the high end of the range (around 2650) when using the PTO, then if it drops under load to 2450 rpms I know I am using to high of a gear for the job. So I guess you're asking if the rpms right, yes I would run it at 2600 WHEN using the PTO, but NOT when just doing other things, drive it like a car. (rpms is IMO, I don't have a hydro, but I wouldn't see why the tractor would need to stay at 2600 ALL the time)