I'm not sure why nobody here mentions it, but BEST PRACTICE in model railroading is to run a feeder from near the center of every...that's EVERY piece of rail...long or short. NS rail is notorious for being a poor conductor. Model railroading involves pieces of rail usually a maximum length of 3' if you're using flextrack instead of sectional track and so it's easy to establish 36" as the maximum rail length per feeder. Also, trusting electrical continuity to little bits of NS sheet metal (rail joiners) between much larger rails is just asking for problems.
Don't ask me how I know this.
Because your slowing is occurring where the track has been ballasted, that's a pretty clear indicator your ballast glue has caused some lessening of the already poor conductive qualities of some (or all) of the unsoldered rail joiners in that area.
If you plan on ballasting the rest of the layout, then you need to take care of both the present problem and ensure it won't occur on the rest of your layout when you get around to ballasting it.
When I finally decided to go DCC about eight years ago, I also decided to get rid of my voltage-dropping long runs of track and my periodical dead zones from soldered rail joiners cracking caused by the stresses of transporting my modular layout to shows several times a year in various types of weather and rough roads.
This meant soldering 6" long 22AWG copper feeder wires to each piece of rail...hundreds of 'em, and running robust power busses to every power district, in my case 12AWG high-purity, fine-stranded, red/black copper speaker zip wire...which is probably overkill, but I'd rather overkill it than it not be sufficient.
Photo (1) - New outboard red feeders being installed on my Echo LDE:Note that in the photo, only half of the feeders are shown. Black inboard feeders and green frog feeders have yet to be installed.
I am going to go out on a limb and say that you have about a 95% chance that your engine slowing is due to not enough feeders and relying on unsoldered rail joiners for electrical continuity. Dirty rail, debris on the insides of the rails cause stoppages, not slowing.
As you can see from my photo, a lot of my existing trackage was ballasted when I decided to do the feeders to every piece of rail. I soldered mine to the underside of the rails after flattening the wire ends and bending them sharply at 90 deg. then trimming them and tinning them. However, they could have been much more easily soldered to the rail web, which is normal practice. I didn't want mine to be seen.
This solved all of my electrical problems and periodically appearing dead zones. In the eight or nine years since I did this, I have never had any of those problems again, which occurred several times a year before I did it.
Another benefit from this was when I went to DCC, I got rid of the rat's nest of wiring underneath and all the toggle switches I needed to throw just to move trains from one block to another using DC.
Since you have a HCD layout, it isn't going to be difficult for you to tip it up on its side to get at your new feeders underneath your layout if you choose to do this to solve your electrical problems. I broke my layout down into its 6' sections and tipped them up one at a time, onto a heavy duty folding table to connect the new feeders to newly installed 14 AWG sub-busses using genuine 3M IDC (suitcase) connectors, which in my experience are more reliable than soldered wire joints, not to mention much quicker. My 14 AWG sub-busses were then connected to the 12 AWG main power busses running the length of each 6' layout section.
Photo (2) - In-progress photo of re-wiring one of my eleven layout sections to DCC after ripping out the old DC wiring:Although I believe what I did was optimal for trouble-free and reliable electrical model railroad wiring, you will probably experience problems feeding your feeders through the holes you drill because of the hollowness of the door your layout is built on, meaning you'll have to fish the feeders through two holes at the same time. If you don't want to supply a feeder to every rail on your layout, you need to seriously consider the minimal solution of soldering every rail joiner to both rails it's joining. A better solution would be to solder a 22 AWG solid copper wire across every two pieces of rail which are joined by a rail joiner. It's also more difficult, but much more reliable than mere soldered rail joiners.
In any case, it appears you definitely need some new feeders from your track to your main power busses...if you have main power busses. If you don't, it's time to install them. For your size layout a main power buss consisting of good quality fine multi-strand copper speaker wire would be the easiest to get, and red/black zip cord makes it easier to keep your wiring organized. I'd suggest 16 AWG wire since you don't have a long run.
Since I was soldering to the underside of already glued-down track much of which was also ballasted, I used my resistance soldering station to do it, and I had to make a special melter-cutter from a wood burning iron to get rid of the plastic tie-spacer under the rail at my chosen feeder attachment points. I don't recommend spending nearly 300 bucks for a resistance soldering station just to attach wires to track, but if you already have a resistance soldering station, here are a couple of photos of the melter/cutter I made from an X-acto #11 blade which fits in a Harbor Freight Tools wood burning kit iron.
Photo (3) - Cutter/melter blade for removing between-tie plastic spacers under the rail:Photo (4) - Cutter/melter in use on RailCraft C55 flextrack already glued down and in use:
Photo (5) - 22AWG rail feeders soldered to the bottom of the rail foot between ties on unpainted Micro Engineering C55 flex:It looks like you need to do quite a bit of soldering no matter what. You might have problems in the already-ballasted area because of hardened ballast glue fouling the joints between rail joiners and rails. A generous alcohol wash and scrub on potential solder spot with a small, stiff brush will get rid of most of the hardened ballast cement (usually either matte-medium or white glue) where you need to solder. You must use an excellent and self-neutralizing flux to both make your solder joints strong and to prevent any future oxidation due to acid remaining on the joint. I highly recommend Superior Super Safe #30 gel available at H&N Electronics here:
https://www.hnflux.com/ For rail joiners, simple lead/tin electrical solder is inferior since this is a mechanical joint, and I recommend a 96/4 tin/silver solid-core .8mm solder, which is about 7 times stronger than lead/tin solder. It's available at H&N Electronics too here:
https://www.hnflux.com/page25.html.
Although the above combination of silver-bearing solder and self-neutralizing flux is much superior to lead solders for mechanical solder joints, when you solder new feeders to your rails, you can use normal multi-core lead/tin electrical solder since this joint isn't mechanical. However, if you're having problems getting the solder to flow properly at the joint, make sure your iron tip is clean and tinned, that your iron is at least 35 watts and use your Superior #30 Supersafe flux...which will immediately solve your soldering problems...really.
I always pre-tin the tips of my feeder wires too, which greatly speeds things up and encourages a good solder joint between the wire and the rail. If you're getting too much solder on your joints, try flattening about 1/4" to 1/2" of your solder with flat-nose pliers, which allows it to heat up faster and makes it easier to apply less.
Soldering all of your rail joiners to your rails and adding more feeders will cure your present and potential future electrical continuity problems, with Superior #30 Supersafe flux making the job exponentially easier.
Have fun!
Cheerio!
Bob Gilmore