If the rear of the guide rod assembly isn't seating so that the plunger can slip through the small hole in the frame, it can stub and stick out too far when the slide is assembled onto the frame. The advice offered by Alk8944 seems to work for most folks.
The 6906 was one of my favorite issued guns over the years. I fired a LOT of rounds through a couple of them.
If you don't mind a couple of my thoughts ...
Keeping the rails properly lubricated can help mitigate unnecessary frame wear.
Recoil & mag springs are recommended for replacement either every 5,000 rounds or every 5 years (of being left loaded in LE holsters all the time). Personally, I like to be a bit more conservative for the smaller compact guns and replace the recoil springs every 2,500-3,000 rounds, myself.
Yes, the 14/15 round 59XX mags can be used in the 69XX series, but as one of the factory folks pointed out to me one time, it's probably wise to remember at some point that the follower is slightly different for the shorter 6906 (although I couldn't see the difference by eyeball after I was told this), which has a faster slide velocity than the 59XX guns. When I carried a `15-rd 59XX mag as a spare for my 6906 I made sure the mag springs stayed relatively fresh and the mag bodies stayed clean and dry. (The 9mm 3rd gen guns seem much more "forgiving" of spring condition and slide velocity than the faster cycling, harder recoiling 40XX's.)
Avoid introducing liquids (solvents, CLP's, oils, etc) to the firing pin and extractor recesses. These areas should be clean & dry, and the accumulation of excessive liquids can lead to the accumulation of semi-congealed grunge & gunk (technical terms
) which can cause feeding, extraction & ignition problems.
The rest of the frame's "internals" do not require lubrication or the accumulation of excessive solvents, oils, etc. I've seen sears become gunked up and unable to freely move and catch the single action cocking notches on the hammers during cycling because of too much gunk in 3rd gen guns.
Keeping the breech face pointed down during cleaning can help prevent gravity from allowing liquids to run into the firing pin hole (and from which they can't easily run back out). Don't let them run into the rear of the firing pin, the bottom of the manual safety/decocker assembly or the plastic & steel plungers in front of the safety assembly ... since those openings are lead to the firing pin channel.
FWIW, a carefully directed flow of compressed air (wear safety glasses!) pointed up into the narrow slot machined into the bottom of the slide, inside the right side channel to the right of the pickup rail (which opens into the bottom of the extractor recess) can blow excess liquids out the side of the slide around the extractor.
The 6906 is a great compact alloy-framed 9mm, right alongside the 3913.