You could physically bolt the heads to pretty much any of the small block engine family. Whether it is good and prudent to do so, that is your choice. Considerations in bore size vs chamber size need to be made.
First, the factory injection system is 'adequate'. If you begin making more power, especially with a large increase in displacement and volumetric efficiency you will find you are dangerously lean. ( increased cubic inches, headers, intake spacer, larger than stock roller cam, low restriction exhaust ) Too lean and you will melt a piston, or have an exhaust valve failure.
The injectors are small pencil style poppets from new, GM has a kit to change these out for a different spider with integrated injectors.
The factory two piece intake and bulky spider inside pose obstacles to making good power. There are manifold spacers available which raise the upper intake manifold and increase the flow around the spider. Or, you can search out the elusive marine vortec injection intakes which have external injectors, and this allows you more flexibility in tuning for the correct # per hour injectors based on the power you are going to attempt to make. Marine intake has no provision for EGR built in.
There is a supplier of higher flow Vortec injector spiders for the OEM truck intake, Wynjammer. They sell them in addition to their supercharger kits.
http://www.wynjammer.com/Vortec_Fuel_Injection_System.html
96-2002 GM 5.7 CP-10722-36-8 36lb $699.00
96-2002 GM 5.7 CP-10722-48-8 48lb $799.00
96-2002 GM 5.7 CP-10722-62-8 62lb $899.00
To use vortecs on a 400, you will need to drill steam holes, or have it done, and then use the correct gaskets. The 400 block has no provisions for a roller camshaft, like the 350 in the truck currently. Yes, you can put a roller camshaft in the 400, you need to machine the block for a cam retention plate and use longer, heavier lifters for retro-fit hydraulic roller cams, measure the pushrod length, and order pushrods. Must use a compatible distributor gear, or tear up the engine when it sends filings through the engine. Must check camshaft to connecting rod clearance.
The cylinder heads will need work in order to use pretty much any larger lift camshaft other than the stock roller out of the 350. You can drop in an aftermarket set of springs, retainers and locks from some websites ( Alex's Parts ) to allow for more lift on the stock Vortec heads. You may have to shim the springs to get the correct installed height. To do this, you will need to buy or borrow a valve spring height micrometer.
Some spring packages will require you to machine the spring pocket, and machine the guide O.D. down for a positive type teflon seal.
Going for much more lift and adding higher ratio rocker arms to the Vortec heads will require you to check the pushrod for interference in the hole it passes through the cylinder head. You may need to drill these out with a 1/2" drill bit.
To get good quench, you will have to deck the block, and run dished pistons to get a streetable compression ratio with the larger displacement.
Bottom line - you could easily put ~ $1000 + into the bottom end of the 400 with hot tank, bore, hone, pistons, resize rods, etc, etc, you can spend ~$ 1000 on a good roller cam kit, wynjammer spider ~$700 -900, exhaust system and headers $ 500, pcm dyno tuning in person ~ $400 +, and on and on.
The good news, is that your engine, if it was the factory engine and no one has changed it, or performed unauthorized repairs, should have Inconel valve seats, instead of induction hardened seats instead of the 1/2 ton L31 cylinder heads. They handle more heat for extended periods than the regular ones 1/2 ton versions got. You also have a better ( not fantastic, but better ) exhaust system than the 1/2 tons get ( larger Y pipe, bigger converters, etc )
To set the distributor base timing correctly, you need a tech2 scanner. Something your GM dealer would have... or maybe someone in the automotive business. Snap-off... Mac, etc is not capable of doing this.
If you change the position of either the crank position sensor or the distributor ( from installing, etc ) you will have to do a CASE relearn on your '99 truck. ( Crank Angle Sensor Error )
Changing out the PCM? You will need to do a CASE relearn as well. Might also want to turn off the factory security measures in the tuning. Unsure what other scan tool devices can command this, but a tech2 will.
My suggestion? Sell the 400 to a circle track racer who wants to make a 377 ( 350 crank in 400 block with main bearing spacers ) and move those funds into other upgrades.
Factory programming in the PCM is well... mild, to put it in a nice way. Tuning, exhaust ( at least better flowing mufflers and tail pipes ) will go a long way to making it feel a bit more stout. Not sure if it is a K series or not, but deeper gearing will also help. Lighter wheels ( stock steel are ~ 40 lbs each ! ) and tires can also help.
