I went through this exact exercise when looking for a mill last year. The 3990 with shipping was $1000 so I decided to step up to a PM-25MV, I am a woodworker and knew I would want the additional capacity. If I had not done that I think I would have gone with the HF mill and had money for tooling etc. LMS sells all of the upgrades and replacement parts. There are tons of modifications you can do yourself if you find you need it.
Knowing what kind of projects you plan on completing will define what machine you buy. As far as starter kit goes I would purchase the essentials such as hold down kit, a couple different size endmills, a vice, calipers, set of good drills, a machinist square, edgfinder and foe from there. I purchased the LMS starter set and found out the endmills are junk and lasted two seconds. I have since purchased high quality endmills as I need them and my results are much better. eBay and Craigslist are great sources for tooling.