Compounds with x are those I know exist but did not get them as of yet.

I'm sure it is random what compounds you get when but I think there are some basic rules for the game to follow where to give what. So by the end of Chapter 5 you should have the following or close.

For 2 FP you will need 150 Circulatory. The same formula works for 4x4 AP:

Basically you need to add as many Circulatory compounds as possible without locking yourself from other compounds.

Please note compound A may prohibit compound B but it might be perfectly fine to use B and then A and get both benefits!

Bolasterone -> Bolandiol -> Cyclofenil = +15
DXAMPEA + AMPEA + BMA + THG + EPO = +61 (please note you have to use THG before EPO)
Gonadorelin + TST = +9 (If you have Anadrol go Anadrol + TST = +24 but blocks Gonadorelin)

85 Total Circulatory so you need agents with 65 base which should be your main agent andquite a few others you might have at the time.

Shortly after I did all this experimenting I have also received Anadrol with +22 and I also decided not to use AMPK with its +22 as it prohibits BMA and few other drugs. Surely you can get 2 FPs withthese as well.

For the 4 AP it is very useful to have the "sprinter" Perk which then adds 4x1 move so you should end up with FP 2 and 4x5 AP agents which is very powerful compared to the 1+2x7 you might have been using without drug abuse.

By Fupp: - 4 AP, 3 FP. +149 Circulatory, +130 Respiratory, +109 Sensory, +91 Motoric. Order:

THG -> AMPEA -> EPO -> DXAMPEA -> Danazol -> Mannitol -> TST -> Anadrol -> BMA -> DHEA -> Bolasterone -> Bolandiol -> Cyclofenil.

Skip Mannitol if not unlocked for 4 AP, 2 FP.

By JamzD_P:
What @Fupp came up with indeed seems to be the most sure way of gaining an agent with 3 FPs. However, if your agent has starting Circulatory of 61 or higher, you could try a different combination, which gives more points overall - 498 vs Fupp's 479. It still boosts you to 200 Circulatory, which is needed for 3 FPs.

Bonuses: C+139, R+130, S+126, M+103, which means 5 HP less, but better Max Awareness, Range of Overwatch and Sight, Awareness regen and lower Dodge cost.

Order:
ampea -> epo -> argoxy -> tst -> xenoxy -> raloxifene -> ampk -> albumin -> igf-1 -> dxampea -> danazol -> mannitol -> anadrol -> bolasterone -> bolandiol -> cyclofenil.

There are two Achievements connected to Body Engineering

1. Scientist - Apply 50 Chemical Compounds

Easily done if you just apply the 10 Compounds you need to reach 150 Circulatory to your top 6 Agents

2. Syndicate Engineering - Engineer an agent with all stats at 140 or above.

This actually popped for me while having 3 stats above 140 and one at 123 but the 123 stat went from above 140 by applying Cyclofenil (-19 Sensory) so the game remembers previous values and once you get 140 it counts for later. (or its a bug)