For HO MU cables Details West makes a cast-metal part, tho I will cut off the "cable" part and replace it with something made from a strand of soft wire. (Side note: I presume that you do mean the "MU cable" and not the "MU hoses" which are different.)
For the handbrake, the choice really depends on your prototype. Again, check out the Detail West or Details Associates parts, and there are other manufacturers.
A molded-on part can be shaved off with a sharp blade, which is a step that must be done carefully and in layers to reduce the chance of marring the plastic (or of slicing up a finger!
). If the new part won't completely cover the area of the old one, then you will have to touch-up the paint. That doesn't have to be perfect (unless you want to do a contest-level model) but neatness counts and you do want to try to get the closest color match that you can.
For couplers the Kadee #58 are near-scale and fit most models (I can't say for sure about the Bachmann, I've never had any of those). The Sergent Engineering are the most accurate HO coupler, a near-perfect reproduction of the prototype, but they will not interoperate with most other types.
As you are new to this my best advice is to start simple and take your time. Good lighting and magnification are a must - you can't model what you cant see!
Reading up is important too. Kalmbach used to sell a book by Jim Volhard called "How to Detail Diesel Locomotives" that was pretty informative. It's out of print, tho you may be able to find a back copy either at Kalmbach, or a hobby shop, or online:
http://www.ebay.com/itm/How-to-Detail-Diesel-Locomotives-by-James-Volhard-1997-Paperback-/151364934466?pt=US_Nonfiction_Book&hash=item233e0d9b42Be sure to post some pics when you are ready! Looking forward to seeing your work!
Ed
