yo J,
Suggest you pull Codes again yourself because too many parts store folks fail to do both the Key On Engine OFF (KOEO) & the Key On Engine Running (KOER) portions; they usually say the Key On Engine Running (KOER) "isn't necessary";
a DIY'er by our good friend, BroncoJoe @
http://broncozone.com/topic/14269-code-reader/page__p__74587entry74587
Post the codes here; sort em by KOEO and KOER;
I run it around to heat the engine up and shift thru all gears incl Reverse.
then; turn off all accessories/lights, etc.
Do KOEO portion first
For Key On Engine Running (KOER) portion, the engine has to be @ normal operating temp.
Post any codes found here or look em up in my broncolinks.com site using the Search feature
And as our buddy Seabronc advised;
Check Timing;
Adjustment in Ford EFI Engines
Source: by Ryan M (Fireguy50) at
http://fordfuelinjection.com/index.php?p=71
Scroll down to; HOW TO CHECK AND SET TIMING