I would be really surprised if you had any trouble at a Schengen border because of that 90 day rule. Especially if you can prove that your travel ends before your passport expires.

If you travel by train between UK and mainland Europe (namely France or Belgium, as Portugal is a bit far), passport controls are not that tight (both performed at the departure station, so in the worst case you're stuck in the UK but without more hassle than that).

However, it may be another story with airlines. There's a chance that you're refused at check-in.