Re: motor swap
The Commander 2000 bulkhead external mount and 3000 bulkhead internal mount are used with a lot of Merc engines and have for probably 20 years or so. They come with an 8 pin pin wiring harness with some additional external wires, two of which (blu/wht and grn/wht) operate your power trim for those units with the PT switch in the top of the handle, that connects inside the engine to the engine WH. The battery hooks up functionally the same as what you have. The battery cables come with the engine and have a good deal of length. My manual shows several variations. If you don't have what I mentioned, get back and tell me what you do have and I will help you with it.
The control cables are pretty much standard. The control box is shifted into N with the fast idle lever disengaged....down for the 2000 and button out on the 3000. This puts your cables ready to accept engine linkage similarly in idle and N. The barrel on the cable (like Max mentioned) is easily adjusted such that you connects the ends of the cables (center conductor) to the engine mounting points and then run the barrel up or down the external threaded brass rod until it will drop into the receptacle provided; both throttle and shift. That should be all that you need.
Mark
