Hey - I just wanted to get some opinions - I currently own a 93 F-250 with a 7.5L that I use to tow my two horse steel trailer that weighs 6000 lbs loaded.  My truck is getting old (294K total miles) and although it is a super cab only has 2 doors -

I found a decent truck that I think will do - eventually we will upgrade to a 3H bumper pull trailer - It is a 99 F-250 Super Cab (4 doors) with a 5.4L V-8 (87K total miles) it is about 6 feet shorter than my big truck.

Should I be looking at a different truck with a larger engine or will this one work?

The 99 5.4 is a weak engine. They switched the valve set up in 04 and increased both torque and horsepower. I had one of the 5.4's in an 03' regular cab 4x4 and it was only rated to tow 7900. I personally towed my horse trailer with it while my 99 Ford F350 with Power Stroke was unavailable. I have a 3 horse Bison Alumasport with 8ft LQ that weighs 7100 pounds empty, and it didn't tow it well at all. According to Ford, the truck your looking at is only rated for 7100 punds max towing in 4x4. Check it out.

https://www.fleet.ford.com/showroom/rv_trailer_towing/2003/2003_SD_F250_350.pdf

In this forum, all will advise to check the rating of the truck and estimate the weight of the trailer you intend to purchase and horses to see if it is within the limit.  The truck you mentioned will get the job done.  Over time, you will be disappointed in the engine on the truck.  This is the same engine they put in the F-150 as well.  Around here, these combinations are only found in commercial applications where a heavier frame is needed and the trucks are not used to carry heavy loads.  Ultimately, they do not hold their resale value.  For that year (1999), you should be able to find a nice truck with the 7.3 in it.  This was a good engine for Ford.  If you can find a good deal on one like this, it will last you for many miles to come.  Plus in the future, if you look to upgrade your trailer (which happens more times than not) you will have enough truck to handle it.  Plus these trucks carry a higher engine warranty than the 5.4 does.  I have had almost all the different engines Ford has thrown in a truck and was well satisfied with my 5.4 F-150.  The most I ever pulled was a 16 ft. stock with two horses and it would do fine.  The 7.3L was one of the most dependable ones I had.  I would not hesitate to buy a used one that checked out to do a good job. 

Many, many years ago, we hauled a two horse CM playday with a 1991 F150 with the 4.9L engine and a 5 speed manual transmission.  It was a long bed and did have the tow package.  Loaded with 1 horse and our stuff, the trailer weighed between 3k & 4k.   On the grapevine on the 5 freeway, north of LA, which if it's not a 6% grade, is probably pretty close in some spots, we did a max of 35mph on the uphill.  The engine pulled strong, but it was just slow.

If the truck has a tow package, it will probably work, but be prepared to go very slow on hills and if the truck has some miles on it I wouldn't be surprised if the tranny didn't hold up for very long.  That Ford straight 6 engine was a great engine (one of my favorites that we've owned), it's pretty bullet proof, but even with a not very big load, it's going to be very slow on hills. 

Edited to add:  Since you've hauled already, I'm sure you already know this but if you get this truck, be sure the check the GCVWR of the truck before you haul anything with it, so that you are sure are not overloading the truck.

I sold my last truck with that engine because I didn't own an oil well.  I got about 5-8 MPG loaded.  Your paycheck will VAPORIZE!

A good deal now but not once you can't afford to fill it up!

So, I will get about the same gas mileage as I have in my F-250 when it is loaded - How does it do when not loaded?