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I have the following loosely constructed army list

Fortification:
Aegis Defense Line w/ Quad Cannon

HQ:
Master of the Forge w/ Conversion Beamer
5x Servitors
Elites:
6x Dreadnoughts with autocannons.

Troops:
2x+ Tactical squads w/ Flamer and Missile Launcher
(?) Sniper Scouts

Heavy Support:
2x Thunderfire Cannons
(x?) Servitors

Now, I hope that this would be considered a decent gunline. My major problems, however, revolves around several key areas. First off, I only have one HQ choice. Should I potentially grab another HQ to keep some of the fire off my Master of the Forge, or throw the points at more heavy support, etc? On the Thunderfire cannons, you can purchase servitors for every Tech-Marine in the army. Should I spend the points on those additional servitors for the cannons, even though they will be mind-locked? I figured I would check, since the only use in that state would perhaps be in front of the cannon as ablative wounds. The third issue is the dreadnoughts themselves. I want to field an even 6, but I am unsure if throwing six dreads into battle armed with only autocannons will protect the army well from aircraft or armor. My fourth problem is manning the Aegis Defense Line. Should I invest in purchasing a squad of sniper scouts and parking them on the gun, or park my Master of the Forge on it? On that same note, considering how many of my units will be able to reinforce terrain, should I bring along more fortifications, or trust in the standard battlefield terrain?

The Master of the Forge allows you to take Dreads as Heavy support also. So you can have 6 dreads but 3 are elite and 3 are heavy. Three thunderfire cannons makes a decent addition to a firing line.

As General_Chaos states, you can only take the extra dreads as HS so no thunder fire would fit
Main problem you face is a lack of anything to deal with AV14, a raider full of SS termies would mash your GL
to your questions
1)1 HQ is fine, I use Culn from IA9 in my gunline as he gives all my tac squads FNP for free! if the CB is killing stuff you wont draw fire from it
2) Servitors IIRC cant join a thunderfire so cant act as ablative wounds
3)6 rifle dreads is good, 6psifle dread is better, this list is better suited to GK to be honest, they dont need the MoF to take 6 and can have higher St (to kill raiders)
4)If the MoF is on the gun he cant use the CB, Telion is a good call here, BS6 and can allocate wounds on troops (4 auto cannon shots ouch!)
5)you can only bring 1 fortification unless your at 2000pts?, also you can ONLY bolster ruins

Hope that helps

If you want to keep it pure dreads, mix it up. They don't all have to be riflemen. Add some TLLCs and MLs to deal with heavy armor. I think you're fine spamming dreads, just don't spam riflemen.

Your troop picks are not very mobile, how are you planning on seizing objectives?

Drop the servitors. Just keep the MotF with the scouts behind the ADL. Keep both him and the sarge in contact with the quad gun. BS5 with the MotF for interceptor, then he can use his own gun on his turn. If you don't need to shoot out of turn, the sarge can take over. BS4 is only slightly worse the BS5 on the TL'd gun.

Lets see here then...

If I remove all potential servitors from the list, that is roughly 200 pts. Considering the list is designed for 2000pts, I should have plenty of room for the Thunderfire cannons after the 6 dreads are slotted in, right? If you guys could do me a favor, and have the codex handy, throw me out a list of what you would upgrade each of the six with, with point values per model. I'd toss out my own ideas, but a buddy borrowed the codex for a week or two.

Don't forget that if you go double FOC you will need two HQs and four troops.

For maximizing firepower, consider a few things (these may or may not match up to your model collection or your play style, but they all provide firepower per FOC slot):

1. Razorbacks for your troops
2. Only run 1 HQ
3. Flyers or speeders for your FA
4. Predators for your HS slots

Each of these can be balanced between anti-infantry and anti-tank firepower, based on your taste and your opponents' tastes.

So, If I converted the list to a 1999+1 list, then how would you recommend I run 4 dreadnoughts, since I figure I should keep both thunderfire cannons in the mix? As for aircraft, I really have no experience with them. In fact, I think I have only fought aircraft once, and that was a single night scythe in a 1500pt match or so.

Thunderfire cannons are pretty sweet in 6th. Cheap, and can kill a lot of troops, even meqs with the high STR ammo.

I've heard idea about a list called "Thunder Storm". Not even sure I know where I heard of it, thinking of one of the podcasts I listen to. But, The core of the list consists of three thunderfire cannons and three storm talons. Fill in the rest as you see fit. I only own one of each of those units and can attest to how good they preform. I can only imagine three of each of those units has to be really good. I have been itching to test it out myself.