Yup, this is tricky, these are steps I go through repeatably all the time.
So the only way a non controlling country can obtain shares of a public corp is to nationalize. What will happen is: The country will obtain all of the current controllers shares. So if IF #1 owns 40% and ENT #1 owns 25% ENT #2 owns 15%, and IF #2 owns 20% the result will be; Country owns 25% IF #1 and #2 will own 40% and 20%(unchanged) and ENT #2 will own 15% (unchanged). And so the only one loses is the one who controls.
If you wanted lets say to have ENT #1 and Country both to own and take fro, the second enterprise you would have to nationalize sell your shares to the enterprise so that both are under the second enterprise. But in reality it is easier to sell to an ENT than sell to a country so have the country be the owner and having the enterprise takeover at the end is definately the preferred method.
As for you error. This is an annoying one, the solution is too have tons of money, but... argh. Anyways what happens here is no matter how much of the corp you want to nationalize it is treated at full value. But there is an added expense, this is probably what is killing you. If the MV is high you have a 400B$ fee to pay on top of it, and mid level is 200B$, low level is 100B$, and if it is really low than you don't pay anything. The money that actually changes hands is only dependant on the share exchange however so if you nationalize 10% of a corp worth a T you won't pay 1T + Fees you will pay 100B + Fees only. And so though you may be able to do 1 at a time you will be able to do them one right after the other because the game thinks you have less money then you actually have.
Now that is how it is supposed to work but I tend to have cash problems on corps that I should be able to afford all the time. So I think they may be something extra the game isn't telling me. But if you really want this done quickly you can drop the MV down pretty fast by manipulating production, or apparently withholding product (not sure how), or the long way but sending salaries real high until the corp start losing money. That way you don't lose money and at least you may see some positive things happen in the meantime. Hope that helped.
Crafty there are a few reasons to do what Baconator is suggesting. One Country controlled Corps don't pay CRU though the country doesn't collect, sustainability to the company or increasing assets for a high priced sale would be a fine reason. Also sending a corp truly public does wonders for it's profitability but at the same time you send away 75% of it's profits, being able to hold onto an extra 25% of them isn't minor.