No, I did not clean up the welds inside. I doubt you would see any difference in performance. Keep in mind, the Ceramic coating is inside as well; if you grind off the welds you are also removing the coating. Also, BBK does not make 1 and 3/4 headers for SN Mustangs with a 5 speed. You can use Fox BBKs as long as you have a Fox transmission, or 3550 series Tremec. I have had both the SN style BBKs and the Fox headers, and the Fox headers fit better by far. The fox headers will hit the clutch fork with a stock T5. I have actually cooperated with BBK to demonstrate the combination of their Foxbody header with a Tremec Transmission. The pictures for installation that the BBK tech team has for this combination are all from my car. If you want to run the Fox headers you are going to have to do some significant modification to whatever intermediary pipe you buy. That being said, I did a direct fit SN header with matching BBK x-pipe on another car not too long ago, and guess what, they didn't fit. I ended up having to crank the inlet pipes together with a ratchet strap. I reused my old Mac ProChamber when I swapped from an SN BBK header to a Fox BBK header. The collectors on the Fox header sit way closer together. The driver's side also comes towards the transmission at an odd angle. I ended up having to cut the inlet tubes completely off, and reconstructing them from mandrel bent tube sections. Keep in mind, all this data is for a 302 block, and while I have no reason to think a 351 Foxbody header won't fit on an SN with a Tremec, I haven't personally installed that combination. Spark plug access on both headers is not restricted at all. If anything, it's better than stock.
Here is that really odd angle you have to do for that driver side header:
This is the completed SN ProChamber setup for Foxbody headers. You can see there is amount of bending or stretching that would get the pipe to fit due to the difference in primary tube lengths and the odd angles. Trust me, I would have tried that if I could. I doubt that Foxbody intermediaries would fit any better due to the drastically different hanger locations.
Kurt