For those that are still having trouble with this game, I think I got the answer, guys!
The secret is: ORIGINAL PARAM.SFO!!!!
I downloaded the game, installed the EXEtrimALL patch, then launched it. Didn't work, as I was expecting. So I figured it out, and here is a small tutorial that should get it working.
1st: With the game already in HD (I only tested internal), go to XMB and install the EXEtrimALL patch through Install Package Files.
2nd: Go to the folder where the above stuff was installed. (HDD0/GAME/BLUS30487/), copy everything inside this folder, and copy everything inside the USRDIR folder too. Paste it in the respective folder (HDD0/GAMES/BLUS30487/PS3_GAME AND HDD0/GAMES/BLUS30487/PS3_GAME/USRDIR.) Remember, everything!
3rd: Download the original PARAM.SFO (you can find it here: http://www.mediafire.com/?8yo5f8oalrzx8yb
) (It's zipped, along with the eboot and other stuff that aren't cracked to run on 3.55, just ignore everything else)
4th: Put the ORIGINAL PARAM.SFO in the game folder where the PARAM.SFO is supposed to be (where you can find PIC1.PNG and all that stuff as well) (my folder is HDD0/GAMES/BLUS30487/PS3_GAME)
5th: VERY IMPORTANT: Fix the game's permissions using Multiman.
6th: Launch the game!!!!
So basically: MGS HD COLLECTION not working > MGS HD COLLECTION w/ EXEtrimALL patch > MGS HD COLLECTION w/ EXEtrimALL patch PLUS ORIGINAL PARAM.SFO AND FIXED MULTIMAN PERMISSIONS = WORKING ON CFW 3.55 FTW!!
(Sorry for the n00b level tutorial, I just wanted to help everyone, even the ones that lack of PS3 expertise.)
Hope this will be helpful!