I can't recall ever having detailed a pre-painted locomotive, although I have done so with pre-painted rolling stock, including so-called ready-to-run stuff. The first step is to remove any things you don't want or want to replace with better parts. Most details which are added-on to the basic body shell can be either "popped" off or cut off - use a sharp blade and take care to mar as little of the surrounding area as possible. If the unwanted details are cast as part of the shell, carefully shave them off using an appropriate blade in your X-Acto. I like the #17 chisel-style blade - it's easy to re-sharpen as needed, and, if you have a Dremel and a cut-off disc, you can create narrower versions of it - clamp the shank of the blade in your vise, then, working slowly to avoid overheating the blade excessively, cut away one or both sides to create the blade width you need to get into a tight space.
One mistake beginners make (some old pros, too) is to use the blade incorrectly - for carving away unwanted details, the bevelled side of the blade should go against the work. That way, if the blade slips, it will skip off the work rather than gouge into it. Also, don't try to remove larger details in a single pass - multiple light ones work better. To speed up such cuts, you can also make multiple vertical cuts into the detail being removed - simply push the blade into the detail as far as it will readily go, repeating until the area is covered, then make a horizontal pass at the same depth as the cuts - each notched segment will pop off as the blade moves along, prevent binding or the need for excessive force.
Smooth any of these areas before adding the new parts - if you work carefully, this can usually be accomplished with the appropriate knife blade - the chisel-type blade is also an effective scraper - hold the knife vertical to the surface being smoothed, with the non-bevelled edge facing the direction of travel, then drag the blade over the material to be removed. You may have to make several passes. In all cases, keep the blade sharpened.
Sometimes the removal of details creates gouges or holes in the body shell - if the new part will hide such a flaw, don't waste time filling it. If you must use a body putty, apply it sparingly - several light coats will shrink less than one heavy one. The chisel blade can be useful as an applicator for filler, too - use it like a miniature putty knife. If at all possible, avoid sanding unless there's no other way to get a smooth finish - sanding sticks can be made by affixing sandpaper to bits of wood or styrene, using contact cement.
If the removed detail leaves a hole in the body shell from its mounting pin, either use the hole to attach the new detail part or fill it with styrene rod. I keep a selection of styrene rod on hand for filling holes to eliminate them or for filling them so that I can re-drill a more appropriately-sized hole for the new detail part. Select a rod that's several thousandths larger than the hole, or, if the hole is too small for the rod available, re-drill it to a suitable size. Using a small brush, apply some solvent cement to the hole (work from inside the shell if possible or use a brush that will fit
into the hole - you don't want to mar the visible surfaces) and also to a short piece of the filler rod. Press the rod into the hole, and push it in as far as it will go - it should stop rather than slide too far. After 24 hours, slice off the protruding stub with your chisel blade and re-drill if required.
Many detail parts have mounting pins - use them - a glued mechanical joint is much stronger than one that's merely glued. Also, use the correct adhesive for the materials involved. While it's tempting to use ca to affix a plastic part to a pre-painted body shell, this is a weak joint that will usually fail - it can be improved if there's a mounting pin involved, but a plastic-to-plastic joint with solvent-type cement will be more permanent. Scrape or sand away paint to make such a joint - chances are the detail part will require painting anyway.
If the detail parts don't have mounting pins, consider adding them where appropriate. Drill holes for a "press fit" in both the model and the detail part, cut a "pin" from suitably-sized brass, steel, or stainless steel wire, then ca it into the detail part, then ca the pin-mounted part onto the shell.
If you're adding grabirons
and nbw detail, do this as two separate operations. I like to add the nbw detail first - drill holes for the shanks of the castings and install them using solvent cement for plastic or ca for brass parts. If using styrene parts, allow the cement to fully harden, usually 24 hours, then drill for the grabirons. I like to use a spacer of suitable thickness to position grabirons the proper distance from the surface upon which they're mounted, then bend-over the wire legs on the inside of the body shell. Remove the spacer, then apply ca from inside the body - if you leave the spacer in place, it can cause the ca to "wick" through the holes, bonding the spacer in place.
If you've carefully plotted and drilled for the grabirons, you may be surprised to see that they appear crooked.
This is caused by the fact that the bent-over ends inside the body shell aren't necessarily in the same horizontal plane as the visible section. This is easily corrected, "by eye", using a pair of smooth-jawed pliers - simply grasp the grab and give it a slight twist in the desired direction.
To paint newly applied details, check to see if the manufacturer of the model specifies the brand and colour of paint used originally - you may be able to get an exact match. Some details will required painting in a contrasting colours, usually allowing you plenty of leeway in selecting something that looks suitable. Make a note of the brand and colour used, so you can paint subsequent rebuilds to match.
The same advice applies when trying to match a colour that you have to mix - keep track of your "test" versions - I like to use the "brush load of this colour, two of that", and so-on to get a rough idea of a paint mix needed, then try it on the model. Once it's dry, you should be able to determine the adjustments needed. For freight cars, of course, an exact mix is seldom required - while there are many versions of "boxcar red", they're all fairly similar. For a diesel, you may want a closer match - many manufacturers offer specific railroad colours, but you'll need to choose the version which you think looks closest and give it a try. Don't be afraid to alter it if required - just use a small portion for your experiments - colour mixing is partly an innate ability, but practice can enhance it. I seldom use paints "right out of the bottle". If you can't get the colour exactly right, don't worry about it unless you're modelling a brand new locomotive - the prototypes got altered with new parts or repaired ones and the new paint wouldn't appear exactly the same as paint that had been in service for some time, either. You might even consider re-painting some things that are un-altered parts of the original model - for instance, if you painted a new horn and a couple of new fan housings in a slightly different different shade of blue than the original paint job, you could also do the same on two or three hood access doors - instant repairs or replacements modelled with only some paint.
Small details can be brush painted - use a good quality brush and don't overwork the paint - most will self level. Allow to cure fully before re-coating, too, or you'll lift the earlier coat. For larger modifications (smaller ones, too, if you wish) use an airbrush. Unless you're looking for a distinct demarcation between colours or between parts of the same colour, don't use masking tape. Instead, use paper or cardstock to shield adjacent areas - cut it to fit around things you're painting and hold it slightly away from the model - this allows a small amount of overspray onto the shielded area, better blending the new part/shade into the old.
In many cases, you'll want to add a clear finish - this can help blend the new paint into the old, or it can make a new (or old) part look as if it truly
is new. For the former, I'd recommend coating the entire model and, for the latter, use masking tape to protect the original.
Don't count on weathering to hide a poorly-done job. While it
can work wonders for poor paint jobs or botched lettering, it seldom covers poorly-fitting parts, sloppy glue joints, or improperly finished surfaces. Work at your own pace (detailing isn't a race) and don't be afraid to re-do something with which you're not entirely pleased.
Wayne