Key Revision 0010 is 3.60. So it looks like you were resigning them with 3.60 keys. So that seems to be the main problem. Oops.
Key Revisions are listed here:
Code:
http://www.ps3devwiki.com/wiki/Revision_versus_Version
If you add the -v switch when decrypting you will see the key revision used to decrypt the file. Might be helpful to check this after you sign a file.
When signing both .self and .sprx files use --np-app-type=USPRX
For EBOOT's use --np-app-type=UEXEC (Update EXEC) although EXEC does work fine too.
I tend to use psn_package_npdrm so I can't say if there would be any problem using psn_force_npdrm and package_finalize.
If you only wish to resign to 3.55 then you are correct about the sys_proc_param on these files, it is already at 3.50 so no need to edit.
For your reference these are the exact command lines I used, however note that I fixed it for 3.40+ fw so the sys_proc_param was edited as well (although I may have forgot to edit the Samurai4.ppuP.self)
For EBOOT:
scetool_029.exe --verbose --sce-type=SELF --compress-data=FALSE --skip-sections=FALSE --key-revision=01 --self-auth-id=1010000001000003 --self-vendor-id=01000002 --self-type=NPDRM --self-app-version=0001000000000000 --self-fw-version=0003004000000000 --np-license-type=FREE --np-app-type=UEXEC --np-content-id=JP0604-BLJS10107_00-PATCH00000000003 --np-real-fname=EBOOT.BIN --encrypt EBOOT.ELF EBOOT.BIN
For Samurai4.ppuP.self:
scetool_029.exe --verbose --sce-type=SELF --compress-data=FALSE --skip-sections=FALSE --key-revision=01 --self-auth-id=1010000001000003 --self-vendor-id=01000002 --self-type=NPDRM --self-app-version=0001000000000000 --self-fw-version=0003004000000000 --self-add-shdrs=TRUE --np-license-type=FREE --np-app-type=USPRX --np-content-id=JP0604-BLJS10107_00-PATCH00000000003 --np-klicensee=2B5C6D1E6F90A53C7831F38A1B0B198B --np-real-fname=Samurai4.ppuP.self --encrypt Samurai4.ppuP.elf Samurai4.ppuP.self