I have a construction underway that is saying it is stalled due to shortages. I have tons of the resource in question. Is this happening because its far away and freighters have to bring it resources in shifts as it builds itself?
If you have construction stalled due to lack of a resource you have plenty of, then the resource is not in the correct location, and freighters should eventually correct the problem.
Pirates occasionally offer me shipping deals. However I cannot see these on the diplomacy screen or ask for more deals from the other pirate I have met. Is this just an invisible thing or is it shown somewhere.
I'm not sure what you mean by shipping deals. Perhaps you mean protection arrangements? If so, protection arrangements do show up in the diplomacy menu as a slightly different color of line under the pirate faction's name and as a positive relations modifier if you select the pirate faction. However, I would suggest that you should be careful of accepting pirate protection arrangements as they are far more expensive than they sound at first - the cost offered is monthly, and the economic summary in the top right of the screen is yearly income. To put them on comparable terms, you have to multiply by 12, meaning that even inexpensive arrangements can easily cost you as much as a couple of small warships or infantry divisions.
Another possibility is that the pirates are offering to sell you information of some kind - system maps, special locations, empire contact, or colony locations. If you or the other empire has hyperdrive, empire contact enables trade, and it will always enable diplomacy, and it's typically cheap, so it might not be a bad deal, though you should remember that the empire is likely relatively nearby and thus should be relatively easily found once you have a decent hyperdrive. Independent colony locations are kind of hit or miss, as pirates love to hang out around independents in force and early on you don't really have the military capacity to seriously challenge a strong pirate faction, but on the other hand an independent colony is just a troop ship away from being a far more valuable and cheaper addition to your empire than a colony founded by your empire will be for quite some time. Special locations can be worth a visit to see if there's any nice free stuff you can pick up easily, like advanced warships (though if these are operational, or if there were some operational warships present at game start, they may have already been claimed by pirates, leaving only the disabled ships behind) or ruins with interesting effects. System maps are basically worthless, especially since you don't know what system the pirates will be selling you a map of, and paying for a map of an empty system is kind of just throwing money away, especially since it's quite easy to map systems yourself once you obtain a decent hyperdrive for your exploration ships. You can ask the pirates to sell you these kinds of things in the diplomacy menu, but if they don't have anything they want to (or can) sell to you the options for these won't be present.
If you want to set up a pirate mission, such as offering a reward to ship in Caslon, then you'll want to select a station or colony and look in the lower left corner of the screen. One of the buttons along the bottom of the selection detail panel is for assigning pirate smuggling missions, which allow you to offer a bonus for importing resources (you can either choose a specific resource or you can leave it as a bonus for bringing in any resources, but you can only offer one smuggling contract per base or colony at a time), and a button to offer a pirate defense mission, which allows pirate factions to bid for a contract to leave a few of their warships at the colony or station you currently have selected with the intent that the pirate faction that wins the bid will use its ships to defend the location for you. You can also offer a contract to attack something you don't own in much the same way. Be careful with pirate missions, especially smuggling missions. They can be expensive (especially the generic resources smuggling missions, though that may not be as apparent since all transactions related to resources come out of the private sector's pockets, including the bonus that you decided to offer for shipping in resources), they can be unreliable or ineffective, and they fund pirate ships that may later be haunting your shipping lanes.
I do have some long chains of freighters. I am currently showing 343k private sector with 49 private ships and 12k in maintance. It shows fuel cost as 0 for whatever reason. My own Ship and base maintance is 16k with tax revenue of 17k so im in the red atm. This may because I have a bunch of these mining bases all around the system. It also prompted me to build a bunch of military that is currently idle 99% of the time.
About the fuel costs, it might just be that the private sector hasn't purchased any fuel yet this year, as the fuel cost is a year-to-date value. The state doesn't pay the maintenance costs for the mining stations; more likely, your base maintenance is mostly your home space port, defensive bases, and perhaps a research station.
I also mined a planet that started almost exactly beside me because it had great gas production, however as time has gone by its getting farther and farther away so that may have been a mistake. Watching a freighter he spent 25 fuel to get there, so 50 round trip. He picks up however 2000 gas. This seems like even if he had to use all his fuel to get somewhere, he would still easily cover the cost. However maybe the problem is maintenance?
Fuel costs vary with trip duration, so even if it's 50 fuel now, it may not be 50 fuel later. Also, unless this is your only distant mine and unless you already have energy collectors on all your ships and stations, the trip between the gas mine and the homeworld is hardly the only drain on your fuel supply. Bases that lack energy collectors will consume fuel over time, which freighters will generally eventually try to replenish and in the process will burn fuel getting to the station. The freighters will also burn fuel going to or from mines for other resources (and be aware that the game isn't necessarily smart about freighter assignments - it may well task an empty freighter at the homeworld to go pick up a load of steel from an asteroid mine even though there is an equally large freighter already on the way delivering fuel, and that second freighter may just end up idling next to the mine for a while after dropping off its load of fuel while the first freighter slowly travels to the mine with an empty cargo hold and eventually back with a load of steel simply because the second freighter wasn't technically available at the time the computer decided to pick up the load of steel).