This is a basic idea, not really thought through, but I think that basic mods should be possible to perform without having to add an attachment – you may disagree and that is fine.
First I think the cost should be between 20-50% of the base price of the weapon. The basic mods allows the adjusting of only 1 characteristic of the weapon favourably by 1 point, no more.
Encumbrance modification could cost about 20% of light weight replacement parts (minimum 150 credits), and require a Hard Mechanics Check.
Hardpoints modification should cost somewhere between 40-50% (minimum 250 credits), and require a Daunting Mechanics Check.
Critical modification should cost at least 50% (minimum 350 credits) and require a Formidable Mechanics Check.
Damage modification should cost at least 40% (minimum 250 credits) and require a Daunting Mechanics Check.
Limitations could also mean that modified characteristics cannot be affected by attachments, or for instance Crit and Damage mods adds the Inaccurate quality to the weapon. Hardpoint modification increases encumbrance by 1 point. Encumbrance mod adds the Fragile quality. Not sure I’d use this, but I thought about it and decided to share the notion.