Business Visas - B Visas do not come alone. There needs to be a Work Permit that is issued by the Ministry of Labor. The B Visa and WP are intertwined and must be processed in a prescribed sequence. The initial B Visa 90 days may have to come from a Thai Embassy/Consulate in a nearby country. A one year Extension of Stay based on the B-Visa is processed by Thai Immigration.
In most jurisdictions, you are required to report to Thai Immigration within 24 hours of reentering Thailand (for reasons other than 90 days reporting). When you report in the 24 hours specified you can ask the I/O to clarify your 90 day report date. And it may not necessarily be 90 days from the date of reentering Thailand.
This has come up before and discussed. At that time my friend and another similar case went like this. Her O-A first year expires Oct 1, 2018. She went to Singapore in late April (only a few weeks ago)... she came back and was stamped in with one year. So her second year will expire in April 2019. She then went to Krabi Immigration and bought a Reentry Permit. She will leave Thailand on June 6 and will not return to Thailand until after the 'enter before date' (first year expiry). Krabi Immigration discussed this with her and said her second year until April 2019 would be preserved.
Seems to me while the OP has little time to do this... A one day flight - to KL and return in about 8 hours - At the KL airport - enter Malaysian Immigration - then go back through - stamp out of Malaysia. Then the return flight lands at Bkk and he is stamped in until May 5, 2019.
I have done the 8 hour turn around at KL Airport myself for other reasons.
Alternately - take a one day land border run on May 5.