I'm not going to cite rules as per what you have, I'm just going to explain the whole Micro Deck IDEA.
So first phase is building your Train. Next you begin the TRAVEL phase by using a "Micro Deck" (This is like 10 cards to start your Deck -- Always the SAME 10 cards by default).
On top of your TRAIN (above) there are PILES of SORTED cards. The CARDBACKS and/or colors vary per pile and when you DRAW from a certain pile, you don't exactly know what you've drawn but that card goes into your DISCARD PILE.
Each PILE of cards represents a certain TYPE of card: Start, Cargo, Crew, and Destination. (This is embryonic and just ideas ATM)
Each PLAYER DRAWS ONE (1) Card from the PILE of their CHOICE and then the 10 STARTING cards plus the cards drawn by the players form the STARTING DECK of the "Micro Deck". The train is now in motion and travelling. Player #1 draws the topmost card from the "Micro Deck" and proceeds to RESOLVE IT.
If it is CARGO, you can place the CARGO card on top of one goods transportation car and that car is now full with "cargo" (let's say CORN).
If it is CREW, you can take on passengers if you have a passenger car and you can earn more money if you have a Bar Car where the passengers can socialize during the trip (for example). Alternatively you can HIRE "Mercenaries" to protect your Train during it's journey. Let say you got "3 Passengers which need to travel '4' stops." You put that card into the DISCARD and then next player draws the NEXT "Micro Deck" Card from the TOP.
Each card you DRAW is a Route Marker and is ONE (1) STOP.
If a CARD is DRAW and it is "Add +1 START card" or "Add +1 CREW card" as the ACTION, you do as the card says and place that card into the DISCARD PILE. And then you proceed to DRAW ONE (1) Card from your "Micro Deck" and resolve it as much as possible.
If it's a DESTINATION and you need "3 STOPS" it means you need to DRAW and RESOLVE "3 DESTINATION CARDS". If you feel like you don't have ENOUGH "Destination" Cards, you can DRAFT from the "DESTINATION" PILE more destinations to ADD to your "Micro Deck".
When you reach the END of the "Micro Deck" you take all the cards in the DISCARD an shuffle them and then THAT becomes your NEW "Micro Deck" with all the extra cards that were drafted from the piles on the board.
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That covers the "Micro Deck", Route Markers and EVENTS. But each PILE has it's own CHALLENGES that need to be overcome.
That's where the IDEA of DICE and a "Tactical" Layer would act as a PUZZLE to open up the game to some RISK and CHALLENGES.
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I guess for now... I won't discuss the "Tactical" Layer just YET... Let's see if you understood the "Micro Deck" CONCEPT and how it can serve as a WAY to TRAVEL from START to FINISH with CARGO and CREW.
If you have any questions ASK AWAY. Because this is only an ADDITIONAL LAYER you ADD to your game. I don't think it needs to affect the game in-so-far that it is something EXTRA to add to enable the JOURNEY.
Let me know if you understand or need further explanation...
Note #1: This is just EMBRYONIC ideas. Things you can take and see if they work with what you ALREADY have. Take them as IDEAS and see if you can ADAPT them to your game or not.
You may need to CHANGE the PILES or figure out alternatives to them that work better for YOUR game. Again I'm just sharing with you some thoughts about HOW you can TRAVEL without a BOARD...
What you have described sounds a lot more like Isle of Trains. It actually has a board! And you build trains and put goods on trains etc. Much closer to your design actually (much closer to what you may prefer in your game).
So, to your idea, you have made it cleaer for sure what you are trying to go for. Dominion deck building with a bit of push your luck when going on the journey. Bad stuff + good stuff get draw and you need to deal with it.
I do not like the idea of players having to deal with another deck, another system, another game haha! It just really seems like two games mashed together into one. It would never work; it is simply too much.
That being said, I think there is still room in this game for variants and expansions. I could see there being a variant where you attempt to build three trains and you take all three on their journey and that is the game. Now, no idea what you would do if one of those trains isn't valid, but hopefully at least one is! Here you could have a personal journey deck (however, building it like you described was like nails on the chalk board! SO MANY CARDS). But again, this almost sounds like a second expansion if I'm honest (if the game is even that successful).
What I am heavily considering is that Journey Deck I desccribed; maybe even in the base game, who knows. Very simple addition that would add an incredible amount of replay value and fun! Now, all of what you said above did stike an idea of possibly putting the shipments/raids/events etc. into the players deck themselves. Sounds cool to draw into a random raid that you know you will need to deal with. But putting shipments in the deck would... again... take away from the experience (players need to see the shipments while building their warehouse deck so they can plan and strategize, if they were randomly put in each deck it would take that away).
Another thing to consider is that the game is already VERY ISOLATING as a player. You pretty much feel like you're doing your own thing. Besides defense. You will compare the defense of each of your trains with everyone elses and this determines who gets raided. Besides this, it feels a little bit like a multiplayer-solo. So, to add another element that would cause players to "do their own thing/their own missions" would not be advised.
I really don't mind chatting about design possibilities; it is fun. But there is very little room for Dead Steam as it is to add anymore systems. Anymore systems and it would burst; very unlikely that a publisher would consider it. In fact, currently, I don't think Dead Steam would get picked up by a publisher. It is already a bit to "sloppy". Most of the game is simultaneous and this leads to a bit of weirdness (players doing things faster than other players, no accountability for actions etc.) This problem and the difficulty of explaining the game straight from the rules are Dead Steam's biggest hurdles currently.