My AT150MLX Cartridge has been misaligned for 4 years

You have probably damaged your records. If a cartridge mistracks - the groove is permanently damaged.

You might want to change your moniker.

HI,
Way off? 
I assume your previous protractor was showing something else otherwise your records would not sound great tiil end of record side, so your cartridge was not sounding so great and was missaligned to start with. Still after setting with the new protractor sounds better but not perfect?
As chakster@ pointed out this is a micro line stylus and needs attention in setting up, not only HTA but VTF, VTA.....
If much better at record inner grooves you are on the right path. New tubes need time to settle and please try to make one change at a time.

Hey,

Thank you for the replies I will address each below:

@petg60: By perfect mean I am still experiencing some harshness on some records but the overall tonally quality is much better, things seem more controlled the bass is more defined. Again the system always sounded really nice but I knew I was lacking something within the setup, I felt it was just the pressing or this or that and I was tried on spending money. LOL, but once I changed the tubes and demo"d some records that never gave me a problem (again the inner grooves issue was not on every record) I was really impressed with what a two hundred dollar upgrade could do.  Even my digital music smooth up a-lot.

I do think Im on the right track I hope...

@chakster my overhang was too forward on the tone arm when I first got the TT I downloaded from Vinyl Engine a Stevensons protractor. I always found the bass to be off (not powerful or sometimes nonexistent) on some records. Also the inner grooves on used records was bad most of the times.

@dover Im not so sure about that because, the handful of records I have been playing since the adjustment which are records that always sounded good sound better and the ones that gave me problems seem to have cleaned up a bit. (but I still get some sibilance and harshness at loud peaks, again its not nearly as bad at it was say 48 hours ago) and Hardy Har Har :)

(but I still get some sibilance and harshness at loud peaks

You’re using a Rega 3? The arm has no VTA adjustment which is a challenge dialling in a cartridge with a fine profile. It sounds like it could go a tiny bit lower at the pillar end. You could try a shim above the cartridge. 

Yes P3 I do have the ringer spacer that Rega makes.