Hi,
I have about year and 3-4 months experience with MPC5748G.
If you never worked with e200 cores, I'll suggest to study core manual as well, especially exceptions (IVOR 1, 5 & 6 in particular, these ones you'll hit easily). Be warned, not everything inside core RM is available in MPC5748G, check core RM vs core related part in the MPC5748G RM.
Then make yourself very clear which MCU revision you are using - 1N81M or 0N65H. There are many differences in peripheral addresses and functionality available. Be aware that 0N65H is not described in the RM since rev.2 (no, you cannot have this revision, only last one is available for download).
Other option to support your effort is community here. There are great professionals, supporting our endless efforts to fight this beast.
You can take a look also at http://cache.nxp.com/files/microcontrollers/doc/user_guide/MPC5748GEVBUG.pdf?fsrch=1&sr=5&pageNum=1
Regarding your questions in particular:
1. I don't think so, when Freescale and NXP merged many documents, previously available disappear from NXP version of website. Now one by one they are published back again (twice or triple as size, because someone (very "smart" by the way) decided to place NXP logo on EACH single page). In comparison, original document contains Freescale logo on first and last page only... So, no one knows how much time it will take to have everything back in place.
2. I think you can give a try to RAppID. If you have chance to have contact with NXP/Freescale FAE, use it!. You most probably will need it many times, especially if you are not willing to give a little fortune to Vector, EB or someone else for AUTOSAR stack or OS/drivers.
3. Use Excel file, attached INSIDE the RM. Yep, I've faced "PDF attachment" feature when I started to work with Freescale and never before...
Last remark, if you insist, you could go with S32 & P&E Micro debugger, but if you want to live long and joyful life, consider changing at least the last one with real debugger, Lauterbach for example. Your life will be much easier and happier, I'm quite sure about this.