I have been reading about tuning the LTFT's by disconnecting the MAF and logging. I have also been reading about scaling the maf to get your trim's correct. Do I need to do both to get the tune done correctly or will just scaling the MAF by % work since I plan on keeping the maf in place?

This is for my 04' HD truck, the only mods are a UPD intake and Magnaflow catback.

 

Since you basically have a stock engine, I would leave the VE map alone and scale the MAF table to bring the LTFTs in line.

 

The fueling is influenced by the VE table more and more as you go bellow 4,000rpm. Tuning your VE table while just cruising around in daily driving and idling scenarios should be good enough. Then, re-enable the MAF and fine tune part throttle as well as WOT fueling by adding/subtracting to that where needed. As stated before, if you're close to stock, it shouldn't take much.