The weapons in and of themselves seem reasonably balanced, but the engines are very much not. It is reasonable to mix mod and original weapons, which is a sign that they've been done well. Stock weapons (except missiles) are just better brawling weapons while the plasma weapons provide better range and the beam turret and railgun are good for precision targeting. Everything except possibly the stock missile launcher (or possibly the plasma missile launcher) has a place.
But the plasma engines are just plain better and there's no reason to use stock.
Your small thruster matches the performance of the stock medium thruster for 3/4 the fuel and is as compact as the stock small.
Two of your medium thrusters have the same space and exclusion zone as a stock large, have 25% more force, and consume 20% more power.
The Large Plasma is superseded by the Forsage Plasma where exclusion zone doesn't matter, which is just preposterously good.
Two of your huge thrusters fit in the space and exclusion zone of three stock large thrusters, put out 146.7% more force, but consume only 53.57% more power.
The Forsage is a good idea, occupying more space in the ship, but this is sabotaged by having doors in places that allow it to extend out the back of the ship without impinging on interior design.
I would suggest that to balance properly with stock, the small, standard, and large have to be cosmetic, the huge should lose half its force and consumpion, and the Forsage should lose all doors except the one on each side closest to the nozzle so that its length actually impacts ship design.
The Antigraves are similarly just too good. The smallest internal thruster block has 300 force (600 using small plasmas) in each direction and takes up almost as much space as four large antigraves that produce 2000 force. A 400 by 1000 force block of small and large thrusters (800 by 1600 using small and standard plasmas or 800 by 2250 using small, standard, and huge if you're using an even number of blocks to balance thrust) is the size of four large and three standard antigraves that produce a total of 2600 force in all directions. Possibly antigraves should have a force advantage over internal thrusters, but not that much of one and not with the same 1:1 force to fuel ratio as stock thrusters. They have little in the way of drawbacks compared even to the overpowered plasma thrusters.
When you come to doing shields I would hope you design them like the guns not like the engines. Narrower arcs projected at longer distances or shorter ranges with smaller or no exclusion zone. Or being higher capacity but slower recharging or in some other fashion filling a different role from stock shields rather than supplanting them.