The slides are precision-ground to fit their bores. A high tolerance fit for the sake of this discussion. It is not unusual to see very fine vertical scratching on the slides due to years of operation. I consider this in itself to be of no concern provided the scratches have no raised edges. Deep marks indicate that dirty air has made it into the carbs caused by a dirty or damaged air-filter or serious leaks in the air-box/air-filter system. I've rebuilt carbs that from the outside would turn your stomach but generally speaking the slides have not reflected the over-all deteriorated condition. In fact, the two worst looking sets of carbs had slides that were no worse for the beating and all slides had freedom of movement.
Varnish as pointed out is the biggest culprit for causing the slides to not move smoothly. My approach has always been to wipe the slides and bores with a soft clean rag and lacquer-thinner and have found that to be all that was required. I would not under any circumstances do anything more aggressive unless there was some physical damage such as very bad deep-scratching. If the slides are sticking as a result of foreign material damage then a very cautious approach has be considered.
I don't concern myself with keeping the slides mated to their bores. Experience has indicated that any slide will (should) fit any bore. The reason for registering a slide to a bore (keeping the slide and bore oriented as a pair) would be if that slide is hanging up. The reason must be first determined and if it's due to abrasion then that slide and bore should be dealt with as a single unit/issue. Attempting to exchange and swap a sticking slide from bore to bore could conceivably do further damage to the slide AND the re-assigned bore. The slides should be tested individually, without being in the diaphragm hanger and with the needle assembly removed.
The slides have an anodized finish which will show some signs of normal wear indicated by shiny areas. IF you must address some marks discretion has to be used. Do not use a polishing wheel as it will remove material very quickly. As pretty as the slides would look, polishing to a bright finish will diminish the fit quality and that will have an adverse affect on engine operation. Some quality "FINE' polishing compound on a piece of soft cloth (Tee-shirt material) wrapped once around a "Popsicle stick" should burnish the scratch edges. A little at a time, test for fit and freedom regularly. Address only the area of concern. If the bore is of concern then a similar treatment using your finger in place of the Popsicle stick will have to suffice. NO - Do NOT use a brake-cylinder hone ! ...........because I know someone will ask ! The idea is clean-up an area of concern - not re-tool the part(s).
It is common for the needle to not align perfectly with the high-speed jet when installing the slide/needle assembly in the carb-body. If the needles are looked at with a jeweler-loupe areas of contact with the high-speed jet can usually be seen where the needle sits "at idle". NOTE; If the needle(s) show wear/deformation as a result then the needle(s) should be replaced. This contact should not impede slide movement. If it does then the needle is installed/retained in the slide, incorrectly. I have seen many carbs with tiny marks all around the high-speed needle. This is from a lack of care in aligning the needle into the jet correctly during assembly. The marks are not of concern as much as any damage to the point of the needle would be.
DO NOT oil the slides ! They are meant to operate "dry". Don't try adding "a spring" to the top of the diaphragm. You are not smarter then a Mikuni engineer!
Hope this helps !