Where would building the Javelis frigates fit in?
Before researching your fleet capacity upgrade. Perhaps I wasn't clear before: do not build 20 cobalts. You can build 3 or 4 to help with colonization, but don't make them the backbone of your fleet. The only time to build large numbers of cobalts is if your enemy is spamming carrier cruisers or flak frigates, which usually only happens online. If you're ready to build a proper fleet of reasonable size, upgrade to Javelis right away and build 20-30 of those.
Secondly, don't wait for your fleet to start your colonization. Send your capital ship out immediately to acquire planets. Heck, you can even go so far as to send your capital ship in one direction and a few cobalts in the other direction to colonize planets quickly. There are usually a few planets with low militia counts nearby that your frigates can handle without capital ship support.
Thirdly, your plan should always be based on what feedback you're getting from your scouts. There is the off chance that you will begin in a position with few ice and volcanic planets, in which case you might seriously consider delaying civic labs altogether and going all-out military. Even if there are a couple of ice or volcanic planets nearby, if they have high militia counts or are out of your way, you might just save them for later. Similarly, if you encounter an enemy nearby (this happens very often on larger FFA games) you may want to go all-out military.
Just another side question, I played a FFA Diplomacy and got lost. In the first 10 minutes, I was getting missions from the AI. What do I do? Continue colonising and expanding my empire or complete these missions?
When learning the game, you may want to change the settings to "locked teams". The AI's will not give you missions in this setting and will not be able to form alliances between each other. This is just one less factor you need to worry about when you're still learning the ropes.
In general, you should never stop your expansion in the early game for any reason except to attack or defend. In the long run, having a large empire pays off spectacularly.
I keep getting hammered by Advent fleets with massive numbers of fighters and bombers. Combined with a perception that I'm doing very little actual damage to their ships (it seems to take forever to knock holes in them), it's somewhat frustrating.
Does anyone have any suggestions on how to deal with mass assault by bombers?
I presume you're TEC. The way you described it, you allowed the game to go on way too long. The longer the game goes on, the harder it will be to win as TEC. They're very much an early-hitter faction that depends on building a superior fleet and economy to overpower the enemy. Once the tech tree is mostly done and the fleet cap has been reached, TEC has almost no advantages over Advent and Vasari.
The answer to huge swarms of strike craft are actually capital ships. Each faction has one capital ship with a special ability that is custom-made to punish massed strike craft. For TEC, this is the Kol with flak burst. This ability will damage all strike craft in the area of effect. Unfortunately, it takes 2-4 bursts to kill depending on the type of strike craft and the level of your Kol. So you will need to complement that with other units. Vasari and Advent have it easy; their special abilities actually shut down the bombers for a short period of time, whereas TEC are still taking the full brunt of that damage until the bombers are killed.
You'll need a large formation of gardas, and having your own carriers equipped with fighters is a good idea. Two Kols with flak burst (preferably upgraded, though that might not be feasible) will be able to deal massive damage to the swarm of bombers making it easy for your other units to finish them off. However, you will need to time these abilities perfectly so as to hit the maximum number of bombers with each burst. If left on autocast, flak burst will be wasted on small groups and will be on cooldown while the main swarm is overhead.
Beyond this, damage dealers are the other side of the equation. TEC is the lowest damage dealing faction in the late game, but the Javelis LRM and Kodiak Heavy Cruiser still pack a competitive punch. Back them up with hoshikos to keep them alive and you can win battles of attrition quite nicely. As TEC in the late game, however, you have to be aware that you're a faction of attrition. You can't overpower a fleet of equal size and you'll need to win by being able to replace your casualties faster. Be prepared to lost and replace capital ships, as well.
Getting high level capital ships is a high priority for TEC. TEC capital ships are fairly weak in the late game, having few fleet support abilities. However, if they can reach level 6 this changes and they become very powerful. The Marza and Akkan in particular have awesome abilities when they reach the highest levels, and the Dunov and Kol have great level 6 abilities as well.