There's effectively nothing you can do about your metal income, besides acquiring more metal extractors.  TEC and Vasari at least have refineries, but Advent doesn't have anything (technically you have "resource focus", but it sucks).  Your best bet at this point in the game, if you can do it, is to raise your credit income with a better trade route and more trade ports, and pick up the slack on the black market.

Now, I don't know what difficulties we're talking about, but the AI on normal difficulty it doesn't surprise me that one of your AI allies is somewhat incompetent.  The AI has a bad habit of getting large sums of money tied up in unnecessary expenses, and on lower difficulties (where it doesn't get a resource cheat) this can easily result in its basic needs going unmet.  Not much you can do about that, either.

Diplomacy pirates are a bit of a nasty opponent, but you do have some good options.  If your starbase is well-placed, you can upgrade it with either mass disorientation or meteor control.  These abilities will do a lot to blunt the pirate attacks, and if this frees up enough of your fleet to continue your attack it should be sufficient, but a more permanent solution is to shut down the pirates entirely.  Best way to do that is to play on the pirate's two big weaknesses: they have no strike craft, and no long-range units.  Get some Iconus Guardians with repulsion to keep their frigates out of range while you rip them up with bombers, which they have no good counter to (just a few flaks).  Snipe out the siege-type units first, then build a starbase.  By the time you units run out of repulsion, the starbase should be complete and help you fight off the remaining pirates.  The turrets are a bit of a challenge, but bombers will eventually whittle through them and then you can bombard the base and finish the pirates.

Now, I don't know what you're up against with the enemy AI, but generally the best solution in these late-game scenarios is big swarms of bombers.  Leave a PJI when you go to attack, and if the enemy counter-attacks, you come back and you smash them with bombers.  Even if they just retreat, you should kill a big chunk of their fleet while the PJI holds them up.  Bombers are also great against starbases (including the mobile Vasari one, since your fleet can just keep moving away from it while the bombers pick it off).  Complement this with a Halcyon Carrier for telekinetic push and a Rapture Battlecruiser for concentration aura and you're in business.  To take on an enemy fleet, a Progenitor Mothership or two with shield restore backing up a fleet of iconus guardians, defense vessels, and destra crusaders is a great tanking force that will be very difficult for the enemy to bowl over, and should protect your carriers if you need that.

For metal, choose the Volcanic planet you own with the most asteroids, upgrade all the logistics slots to fill with trade ports, set them to resource focus.  Then place a starbase, and get the two upgrades that boost the planet's allegiance (can't remember what the ability is called.)  If you have more than one Volcanic with three or more asteroids, rinse and repeat.  For the front line, don't forget the Mass-Disorientation upgrade to your starbases. (maybe this is obvious)

Of course, if you don't have any Volcanic planets, this won't work.  I might choose the planet closest to my capital planet that has two metal roids and do the above there (the allegiance will be highest closest to your cap planet, of course.)  I've had to do this once or twice; it sucks, but it will boost the rate somewhat. (I'm assuming you've researched metal extraction rates.)

"I'm assuming you've researched metal extraction rates"

Are the upgrades to metal / crystal extraction rates really worth it in most games? Seems like some of those 5% upgrades won't pay off for like 2k-3k seconds which is a long time imo. Just curious since I usually trade port spam and use the black market egregiously just like Darvin3 pointed out. 

Yeah when I crunched the numbers for medium maps, the upper extractor bonuses seemed underwhelming. Yes they would pay off in like 45 mins, but I always felt like I could funnel that into larger fleets or overclocking my trade network to get to victory faster. Granted this wasn't always the case (meaning I didn't win as fast I had hoped) but it is what I 'thought' at the time.

You could also sb those 2 planets your fleet is defending. AI is stupid and will surely attack directly into that sb. Level ur caps up and when they loose their fleet counterattack and sb next planet straight away. That way you can go 1 planet at the time. 

This strategy doesn't work with vicious AI. He replaces his fleet as you can kill it (ship production cheat that he has) and only somehow works with cruel and unfair AIs. 

Bombers en mass are good solution and wiping pirates off is a good one as well. Be sure though that you stay out of range of those turrets when u are dealing with pirate fleet. They do something like 50+ damage. And keep your bombers on hold position when you are killing pirate ships.... They do some massive damage to bombers as well.

From the sounds of it you have basically been caught in a defensive rut. Youre trying to hold your ground on multiple fronts and your fleets and economy cant keep up with the pace and are slowly being worn down.

Ive been in this position before If you keep as you are you WILL loose. It might take a while but eventually one of your fleets will become so thin that one large attack will smash it to bits and when that happens you'll start loosing colonies.

When I got into this situation I found the problem was that fact that I was attempting to stay on the defensive and trying to spread my fleets to defend every front. From the sounds of it you havent the recourses to do that so the only way I can imagine to prevent your eventual defeat is to go on the offensive.

In my game I pulled ships off sectors I was trying to defend and formed them into one large fleet. I knew it as risky because it was leaving systems open to attack but I formed the fleet anyway and took it straight into enemy territory, struck hard, took a colony and moved on to the next one.

The effect totally devestated the enemy force because suddenly they had gone onto the defensive and since they were between attacks the AI hadnt built enough ships to hold such a sudden and brutal attack and the loss of those recourses meant they couldnt respond effectively.

Basically that one large, hard hitting strike turned the tables. Its risky but I think you should try it.

Madcat plz tell us how you got on im properly into this story now lol