Since the relegations are unbalanced, you're going to get weird results. Right now, the NIPL is acting as a giant pump. Since it's sending a team to the EPL, it needs a team to replace it, and since it receives no team in relegation, a team has to swap from another league. I'm guessing the Watford -> St. Mirren -> NIPL winner thing happened because Watford was because Watford was either the lowest finisher or last alphabetically[, assuming West Ham went up]. I'm sure St. Mirren was chosen because it was closest geographically to Northern Ireland to replace the NIPL winner, and were in turn replaced by Watford, the "extra" team in the Championship based on whichever criteria the game used.
Basically, one season, after promotions and relegations, would leave the NIPL short a team, since it's sending one more team than it's getting, and the Championship with an extra one, for the opposite reason. It's going to grab the geographically closest club for the NIPL, and boot out the extra team in the Championship, based on whatever criteria it uses, and either send it to the NIPL, or through Scotland if it's too far.
That said, even if you balanced the relegations, you're still going to get some weird exceptions, since it's not guaranteed that the correct number of clubs from each nation will be relegated. The game is going to plant the relegated teams in the league which is closest geographically, so Northern Irish teams will be relegated, they'll just be sent to another league. They'll probably be used the next season as the team which gets shuffled to fill the NIPL void. You'll also get some trapped in other leagues, since only one is returned home every year, and I'm assuming you have more than one in the EPL to start with.
In all likelihood, your EPL is going to end up very English with a few Scottish teams and the NIPL winner[, though there's no guarantee they'll be Northern Irish]. Most Northern Irish and Scottish clubs are probably not good enough to stay up long-term, which I think is the reason you went with fewer relegations there. The only way to really make it work to either roughly level out all the teams financially and talent-wise beforehand, so they aren't at such a disadvantage, or have the EPL relegation places and NIPL and SPL award loads of money so the lesser clubs can grow financially and begin to challenge. Think of it like the current EPL-Championship divide. Most promoted teams aren't able to compete financially, and slip back. That said, the gulf is slightly lessening, as more Championship clubs have won promotion and have been able to build with the parachute money, but they don't really make enough to challenge at the top.
Until you find a way for the smaller Scottish and Northern Irish teams viable in the EPL, you're going to have them lasting a season before having to shuffle around for a year or two and making another run.
Basically, balance the promotions and relegations, and get the smaller teams up to at least Championship standard, so they don't end up in a strange league by all being relegation fodder. I hope you can get it to work, at least somewhat!