I think you answered your own question. If you can get the latest for about the same price, why not do it?
1. The 5-speed 5R115 "Torqshift" is a nicer-driving transmission. We have 4R100 and have driven the 5R. To me it isn't the extra gear, but the overall shifting behavior of the 5R that sets it aside
2. That heavier axle has substantially larger brakes and I believe it also incorporates stronger ball joints. Old axle is rated 4600#. New has an improved front sway bar. I'd say the need depends on the front axle loading of the specific coach you're considering. You WANT a well-loaded front axle, say 75% or more of its rating, to have good handling and tracking. Recent weight on our coach showed 95% and I'm planning to replace the 4600# axle with the 5000#.
3. And you missed one: The "early V10" from 1997-99 was well known for sparkplug thread problems which were "corrected" starting 2000 (CHASSIS model, remember, may be earlier than COACH model), BUT some of the corrected heads (called Performance Improved or PI) were not machined correctly and problems lingered in a small portion of the engines. If you get one new enough to have a Torqshift, you're also beyond the years where some PI heads were troublesome.
2008 chassis and up gets you into all the above improvements. I believe 2005 and up gets you all but the axle.
