If you didn't grind at all this can be a little tight depending on how your setup is (congratz on getting this far though). The first wave of aliens have to be fought off, iirc there are 2 frigates. The second wave (right before you reach the portal) will actually be auto-destroyed by the script if I'm not mistaken. You're talking about the dash to the mobile Alien Portal right? That's the only 2nd portal in the Precursor system.

Have you tried letting your mothership hang back while your pilots weaken the enemy? 2 shields should be more than enough on the mothership, but I think I'm thinking of the maxed one (Kali?).

You're going to loathe the game 2 systems out, though - when you return to X220 there'll be a pretty large portal ambush by berserks ("large" as in there are capital ships present). Since you haven't grinded at all, you may benefit from breaking away to do a little as soon as you pick up Joseph. Not sure what to recommend, how's your team setup like? E.g. average skills, ships, equipment. Aliens aren't too hard except for those damn torpedoes and the frigates' lasers seem to be able to fire non-stop.