1. The trans has to be removed so you can see the flange and determine which flange is used which determines which bearing is behind it.
2. The LN dual row IMS is really now thought to be capable of much much longer use than was originally thought. The figures LN gives you are mostly lawyer dictated. Is The Solution the best? Yes. But if it were a LN dual I wouldn't worry. (If it were a car I intended to keep forever, I'd do The Solution but then I'd also address all the other week points known and those run the costs up to far more than buying an excellent replacement car.)
3. Suspension refreshes can be done as they appear to be needed or all at once.
4. The 99 blocks were not porous. Only 97s. The 99's were subject to slipped sleeve issues but if it hasn't happened by now.... (I haven't heard of one in years)
More info
here
I've been following the IMS issue since before it was public knowledge. I've bought two Boxsters, a '99 and an '01S. Both wonderful cars. I was more worried about their basic maintenance than the IMS (not that it can't happen and not that it won't be very expensive if it does) and promptly put probably $3k into my second Boxster to bring it up to my standards (brakes, tires, 90k service, alignment, fluids) and then drove it very close to daily for 5+ years with no issues. Wonderful reliability (better than same year Honda). Two owners later it was still on its original IMS last I heard. I should also say I wasn't cash constrained and would have put in a $20k+ total upgrade engine had the engine failed but with a 1% per car year failure rate I could afford to gamble.
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