I tried both your v2.6 and the new v3. While v3 is at least giving consistent sizes, I'm still getting the 4100 when I try to install. And for good reason I guess, the resulting .wad is exactly 64 bytes bigger than the original. I'm not sure why this is. So far I've only been trying to do NES games though. I'll have to test the SNES, TG16, and Genesis options and see if they do the same or not. There's not much for N64 I want to inject other than Goldeneye (which requires a special hack as previously mentioned, and even then it still won't save if I read that right). For some reason the GUI always hangs saying it's waiting for the final wad, but the wad is there, and it's complete. Well, not hangs, I can hit cancel, it gives me an error 53, and then quits, so, maybe "eternally waits for some unknown process to complete" would be more accurate than saying it "hangs" on me. If I run the command line utility it completes successfully. The same wad is generated by both and at least it's always the same size this time, even if it is the wrong size and an extra 64 bytes is getting in there somehow.
Update: It's doing the same thing on Genesis injects -- the resulting file is 64 bytes bigger. And when it comes to battery backed wads, don't use Sword of Vermillion, it really isn't big enough for Phantasy Star II even, lol. Sonic 3 is your best bet. BTW, from what I can tell there isn't a wad big enough for Phantasy Star IV so forget about it until they put something like Sonic 3D out for VC. Oh, and same result trying to install it, the (ret -4100) error strikes again. Well, time to see what is being added to these files and where, I'm injecting Final Fantasy into Kirby's Adventure next because I have one that works to compare to.
Update 2: The wad packer is doing strange things. It puts an 06 at offset 0B (should be 00, had to change that). It adds 0D at offsets EE, 373, 422, 45A, 534, and 954 (that's EE, 372, 420, 457, 530, and 94F if you delete as you go). It also adds 00s from A47 to A80 that shouldn't be there (A41 to A7A if you already deleted those previous 6 bytes). Deleting these makes it the right size, and after figuring out that 6 was there and changing it, the wad finally works as it's supposed to. I've been using the command line utility of course to avoid the "waiting for final injected wad" thing, though technically the GUI does produce the same wad in spite of said error. Hope you find this information useful and are able to figure out what causes this so I don't have to keep hex editing them manually. Meanwhile I'm going to try making a PPF. Never mind, that won't work, the sizes don't match. Guess I'll just keep removing those 64 bytes and switching the 6 to 0 manually.
Update: It's doing the same thing on Genesis injects -- the resulting file is 64 bytes bigger. And when it comes to battery backed wads, don't use Sword of Vermillion, it really isn't big enough for Phantasy Star II even, lol. Sonic 3 is your best bet. BTW, from what I can tell there isn't a wad big enough for Phantasy Star IV so forget about it until they put something like Sonic 3D out for VC. Oh, and same result trying to install it, the (ret -4100) error strikes again. Well, time to see what is being added to these files and where, I'm injecting Final Fantasy into Kirby's Adventure next because I have one that works to compare to.
Update 2: The wad packer is doing strange things. It puts an 06 at offset 0B (should be 00, had to change that). It adds 0D at offsets EE, 373, 422, 45A, 534, and 954 (that's EE, 372, 420, 457, 530, and 94F if you delete as you go). It also adds 00s from A47 to A80 that shouldn't be there (A41 to A7A if you already deleted those previous 6 bytes). Deleting these makes it the right size, and after figuring out that 6 was there and changing it, the wad finally works as it's supposed to. I've been using the command line utility of course to avoid the "waiting for final injected wad" thing, though technically the GUI does produce the same wad in spite of said error. Hope you find this information useful and are able to figure out what causes this so I don't have to keep hex editing them manually. Meanwhile I'm going to try making a PPF. Never mind, that won't work, the sizes don't match. Guess I'll just keep removing those 64 bytes and switching the 6 to 0 manually.

