So, my megasquirt tunes for the 2.9 are posted in the tech forum. Saves you the time and frustration.
The holley system is NOT perfect - it maps the same way that the MS system does, just at 4x the cost. And it gets the engine "close enough," not "dialed in."
There are two main styles of upper, and three main varities of lower intake for the 2.9 - the twin throttle body and single throttle body uppers, and the standard and reinforced Ranger lower, and then the Merkur/Euro lower.
The TTB upper flows about 13% better than a fully ported Ranger upper. As far as performance goes, there is no comparison between the two, the TTB one is just better in every sense of the word "better." Better throttle response, better flow, cooler temps, etc, etc. Look for one off a Merkur, or cruise eBay UK or DE to find a complete one for under $100. I have three of them for a reason haha.
Best bet is to look for a MS DIYPNP 1.5 for Ford 60 pin. Or, a microsquirt, and make your own adapter harness. There is also a tuning shop out by Philly that carries a microsquirt and prefab harness for around $435 all in.
Carbs and TBI are a step backwards from MFI. Neither work as well, neither are precise by any stretch of the imagination, and neither are a cost effective option.
For best results, re-wire your injectors to fire for sequential fuel injection with the MS.
Just my $0.02. YMMV.