Is there a clutch on the current engine? Is the hydro pump direct mounted to the flywheel via a splined shaft and drive plate on the flywheel? is the hydro pump splined shaft driven direct mounted to a drive plate or is there some clutch and shaft driven off the engine back into the hydro pump. Not sure if this makes any sense, but the big question is whats in the bell housing on the cat now and how is the hydro pump driven? Bell housings can or may not be the same, its just what it takes to mount the engine and its flywheel and if there's a clutch on the engine and mate it to the transmission and bolt that up and get the hydro pump drives to mate up as well.
The 3306 you already have, what bell housing is on it now? Did this application ever have a 3306 in it ever from the factory, if not what other engines were put in it, reason I"m asking is time and money factor, if there was a 3306 ever put in it, you can access all these numbers of housing and drive plates, clutches, everything from either bomag or cat, it'll save a lot of headaches. I understand why you want to switch engines, but look to where someone has already done the work for you, even if it'll cost you a higher dollar engine, you'll save it in the long run.
I mated a IH 466 to a hydraulic pump and ended up with an off the shelf bell housing a number two truck housing if I recall, but I had an adapter plate custom made to mount the pump and also a custom made adapter plate on the flywheel to mount an off the shelf spline drive to so the lengths were the same so they could mount up, its been so long ago I can't remember what was different from the custom made plates to what was available that I could buy, but it wasn't much, but what we needed to do to get the job done, but spent a lot of time and plenty of money to figure it all out, thats why if possible ask to find out if anyone has done this before and how they did it, it took me almost a year to finally get it right on that project, after plenty of experimentation and errors first.