Wow! Thanks for the report; As you have noticed, there is a lot of new things in the set, which obviously leads to a lof of these issues.

I have addressed many of them already and the rest you write here I will fix in 0.4.5. Just some comments:
- The monorail express engines ('flow' and relatives) haul 40, 24, 24, 24 passengers capacity instead of the indicated 48 for generations 1, 2, 3, 4 respectively.
Interesting issue, I did not notice this at all, will be fixed to work as indicated in purchase menu.
- Chami express wagons have less capacity than indicated, and have the indicated amount only beyond a certain length.
They have it noted in Chami Express extra info, that they change capacity, the 112 is the upper limit, I will just fill the info with that
- Maglev cargo engines-pulled express wagons have 78 passengers capacity instead of the indicated 39.
(obsoletes all express passenger engines beyond 2000)
That is because these wagons now consist of 2 parts instead of one, but I forgot to change that value.
- Maglev cargo wagons have 22 units of cargo per car capacity instead of the indicated 24.
Wrong purchase menu value, should be 22, 24 is only for SLUGs
- All Maglev wagons weigh 60 tonnes, yet maglev express wagons weigh 20 tonnes. (note: there is no diffrence for rail and monorail in wagon weights)
Interesting find, will unify to 60.
- THE SLUG indicates vaguely 'wagon capacity: 50' yet cargo wagons have 24 units capacity, passengers 50, and mail 28
That is correct, it should just be saying Express wagon capacity. That mistake appeared because formerly SLUGs were express only so it was obvious. Mail is about correct.
- When refitting cargo wagons from passengers to mail/gold/diamonds, the amount of mail it can carry per passenger varies from one wagon/engine combination to the next.**
It is pretty much impossible to unify this ratio exactly as each value fits something else, but I will see what I could do about this in general. So far I filled these ratios rather randomly to be honest.
- There are some engines that lose statistics from having a longer train, yet there is one engine that GAINS statistics. It performs rather too well for trains of five tiles and longer.
This is more or less correct, while they definitely should not perform that well. They should perform well after reaching at least 6-7 tiles, up to 10 tiles with great performance - building 10 tile curves is a pain in the ass.
- The engines that indicate they gain or lose some amount of power do not indicate that they are talking in units of 'hp'. When you have set the SI system, for example, the unit for power is KW, which is different from hp, hence the indicated values are then incorrect.
They are code values without units. For example Power: 5000; I will see what to do with this as the power is only mentioned in the flexible train stats, it isnt that much work to fix.
- The 'dogstar' class of vehicles lose tractive effort per added train unit, all four have different top speeds and powers, yet the same lower bound for their tractive effort that does not increase with later generation engines, making the penalty far more crippling for the later versions than the earlier versions (dogstar* has literally no penalty, while I Choose Noise loses 40% of TE at length 10).
Very, very odd. I have no idea how that came out. I will look at that more closely.
- The 'maelstrom' class of engines loses 2 units of cargo capacity when you add the 15th wagon.***
It is MonoLocal, not maelstrom (MonoICE), it occurs because the wagons reduce capacity and that is some weird treshold, will see what can be done - monoLocal will change stats anyway.
- This class also loses another 19 units of passenger capacity when adding the 17th wagon.***
Same as above
- Chameleon engines, which are supposed to be an 'extra' class of engines, beat the monorail local trains hands down in everything but loading speed for trains >= 5 tiles when transporting passengers (even with the reduced capacity). Yet the monorail local trains are best used for small lengths, which means they are rather pointless now.
I know, capacities will be rescaled again and local loading speed will be capped at 5 stages.
*'Dogstar' itself indicates its tractive effort decreases, yet it (the tractive effort) does NOT decrease with added wagons.
Weird, will check.
** e.g. 100 passengers might equate to 50 bags of mail, and 50 passengers might equate to 28 bags of mail. This ratio can even differ (wildly) between wagons/engine on the same train, making it important to refit certain parts of the train first before others. This amount of micromanagement might turn off users. Worse, when upgrading to a different train class, auto-refitting might give you a sub-optimal consist, requiring a dreadful manual upgrade! An especially egregious offender is the chameleon engine, which refits one passenger = one mail = one gold/valuable/diamond instead of the more often seen 8:4:3 ratio throughout the set. Note: the ratio in the default trainset is 4:3:3.
Yes, completely wildly

I will see what I can do with that but it probably wont change too quickly as there is quite a lot of those things. Will see how it goes.
*** This means that if I'm using a network of local trains of length 8 for whatever reason, and upgrade to monorail, I would have to remove one wagon from each and every one of my trains induvidually to gain cargo capacity. I thought this set had easy auto-upgrading?
Well, yes this is a bit strange, yet it has some logic. The original logic is that the strongest points of the train stats meet at odd values, like 1.5 or 7.5 in this case. Therefore it is considerable to build these lengths for local trains for monorail. I am not sure how will this move, as I will probably be changing their stats in general.
All in all, will be changed or improved in some way. The current versions just brought so many new features that it obviously has to bring also some side effects

Thank you for playing carefully and discovering so many issues.