It really depends on where you go for parts, how many parts you need, and how expensive is the kit itself? If you only need a few parts, you don't want to have to buy an entire runner like HLJ makes you do. However, if you need a tone of parts from a single runner, that may be easier. They charge a percentage of the price of the kit depending on the percentage of the kit you want.
Gundam Store and More charges $2.50 per part and then $5 for each weapon (sword, gun, etc), plus $2.95 for shipping... Buying 4 or 5 parts for a high grade kit, you're better off buying a new kit and keep extra parts for whatever. However, $15 total for a few parts for that MG The O you messed up because you used the wrong thinner and now the leg armor is melting vs shelling out $80 for a whole new one, much better deal. But GSAM will only sell parts from a kit on their "parts list" unless there are enough requests for them to dig into a new kit.
I'm not sure how GG Infinite does their parts orders, but I hear they can get them straight from Bandai. They might be your best bet, if that's the case.
Until Next Time: Happy Building!
Want to Buy LM Leo or Taurus from Gundam Wing, built or unbuilt! Willing to pay big!